PubChem Substructure Fingerprint

V1.3 http://pubchem.ncbi.nlm.nih.gov

The PubChem System generates a binary substructure fingerprint for

chemical structures. These fingerprints are used by PubChem for
similarity neighboring and similarity searching.

A substructure is a fragment of a chemical structure. A fingerprint

is an ordered list of binary (1/0) bits. Each bit represents a
Boolean determination of, or test for, the presence of, for example,
an element count, a type of ring system, atom pairing, atom
environment (nearest neighbors), etc., in a chemical structure.

The native format of the PubChem Substructure Fingerprint property is

binary data with a four byte integer prefix, where this integer
prefix indicates the length of the bit list. For the ASN.1 and XML
formatted data, this property is stored in a PC-InfoData container,
as described by the PCSubstance ASN.1 definition or XML schema:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/

PC-InfoData is able to handle various types of data. Each PC-

InfoData has a PC-Urn object (urn = universal resource name). Each
property has a unique trio of "label", "name", and "datatype"
definition (e.g., for PubChem Substructure Fingerprint, this is
"Fingerprint", "SubStructure Keys", and "fingerprint", respectively).
The fingerprint binary data is hex-encoded, when provided in the XML
or textual ASN.1 formats.

When exporting fingerprint information in the SD file format, the SD

tag for the PubChem Substructure Fingerprint property is
"PUBCHEM_CACTVS_SUBGRAPHKEYS". The PubChem Substructure Fingerprint
is Base64 encoded to provide a textual representation of the binary
data. For a description of the Base64 encoding and decoding
algorithm specification, go to:
http://www.faqs.org/rfcs/rfc3548.html

Below is the description of each bit represented in the PubChem

Substructure Fingerprint. Some fingerprint bit descriptions are
written in SMILES or SMARTS notation. For additional information on
SMARTS and SMILES, please go to:
http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_sp
ecification

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PubChem Substructure Fingerprint Description

Section 1: Hierarchic Element Counts - These bits test for the
presence or count of individual chemical atoms represented
by their atomic symbol.
Bit Position Bit Substructure
0 >= 4 H
1 >= 8 H
2 >= 16 H
3 >= 32 H
4 >= 1 Li
5 >= 2 Li
6 >= 1 B
7 >= 2 B
8 >= 4 B
9 >= 2 C
10 >= 4 C
11 >= 8 C
12 >= 16 C
13 >= 32 C
14 >= 1 N
15 >= 2 N
16 >= 4 N
17 >= 8 N
18 >= 1 O
19 >= 2 O
20 >= 4 O
21 >= 8 O
22 >= 16 O
23 >= 1 F
24 >= 2 F
25 >= 4 F
26 >= 1 Na
27 >= 2 Na
28 >= 1 Si
29 >= 2 Si
30 >= 1 P
31 >= 2 P
32 >= 4 P
33 >= 1 S
34 >= 2 S
35 >= 4 S
36 >= 8 S
37 >= 1 Cl
38 >= 2 Cl
39 >= 4 Cl
40 >= 8 Cl
41 >= 1 K
42 >= 2 K
43 >= 1 Br
44 >= 2 Br
45 >= 4 Br
46 >= 1 I
47 >= 2 I
48 >= 4 I

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PubChem Substructure Fingerprint Description (cont.)

Section 1: Hierarchic Element Counts (cont.)
Bit Position Bit Substructure
49 >= 1 Be
50 >= 1 Mg
51 >= 1 Al
52 >= 1 Ca
53 >= 1 Sc
54 >= 1 Ti
55 >= 1 V
56 >= 1 Cr
57 >= 1 Mn
58 >= 1 Fe
59 >= 1 Co
60 >= 1 Ni
61 >= 1 Cu
62 >= 1 Zn
63 >= 1 Ga
64 >= 1 Ge
65 >= 1 As
66 >= 1 Se
67 >= 1 Kr
68 >= 1 Rb
69 >= 1 Sr
70 >= 1 Y
71 >= 1 Zr
72 >= 1 Nb
73 >= 1 Mo
74 >= 1 Ru
75 >= 1 Rh
76 >= 1 Pd
77 >= 1 Ag
78 >= 1 Cd
79 >= 1 In
80 >= 1 Sn
81 >= 1 Sb
82 >= 1 Te
83 >= 1 Xe
84 >= 1 Cs
85 >= 1 Ba
86 >= 1 Lu
87 >= 1 Hf
88 >= 1 Ta
89 >= 1 W
90 >= 1 Re
91 >= 1 Os
92 >= 1 Ir
93 >= 1 Pt
94 >= 1 Au
95 >= 1 Hg
96 >= 1 Tl
97 >= 1 Pb
98 >= 1 Bi

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PubChem Substructure Fingerprint Description (cont.)

Section 1: Hierarchic Element Counts (cont.)
Bit Position Bit Substructure
99 >= 1 La
100 >= 1 Ce
101 >= 1 Pr
102 >= 1 Nd
103 >= 1 Pm
104 >= 1 Sm
105 >= 1 Eu
106 >= 1 Gd
107 >= 1 Tb
108 >= 1 Dy
109 >= 1 Ho
110 >= 1 Er
111 >= 1 Tm
112 >= 1 Yb
113 >= 1 Tc
114 >= 1 U

Section 2: Rings in a canonic Extended Smallest Set of Smallest Rings

(ESSSR) ring set - These bits test for the presence or
count of the described chemical ring system. An ESSSR ring
is any ring which does not share three consecutive atoms
with any other ring in the chemical structure. For
example, naphthalene has three ESSSR rings (two phenyl
fragments and the 10-membered envelope), while biphenyl
will yield a count of only two ESSSR rings.
Bit Position Bit Substructure
115 >= 1 any ring size 3
116 >= 1 saturated or aromatic carbon-only ring size 3
117 >= 1 saturated or aromatic nitrogen-containing ring size 3
118 >= 1 saturated or aromatic heteroatom-containing ring size 3
119 >= 1 unsaturated non-aromatic carbon-only ring size 3
120 >= 1 unsaturated non-aromatic nitrogen-containing ring size 3
121 >= 1 unsaturated non-aromatic heteroatom-containing ring size 3
122 >= 2 any ring size 3
123 >= 2 saturated or aromatic carbon-only ring size 3
124 >= 2 saturated or aromatic nitrogen-containing ring size 3
125 >= 2 saturated or aromatic heteroatom-containing ring size 3
126 >= 2 unsaturated non-aromatic carbon-only ring size 3
127 >= 2 unsaturated non-aromatic nitrogen-containing ring size 3
128 >= 2 unsaturated non-aromatic heteroatom-containing ring size 3

129 >= 1 any ring size 4

130 >= 1 saturated or aromatic carbon-only ring size 4
131 >= 1 saturated or aromatic nitrogen-containing ring size 4
132 >= 1 saturated or aromatic heteroatom-containing ring size 4
133 >= 1 unsaturated non-aromatic carbon-only ring size 4

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PubChem Substructure Fingerprint Description (cont.)

Section 2: Rings in a canonic ESSR ring set (cont.)
Bit Position Bit Substructure
134 >= 1 unsaturated non-aromatic nitrogen-containing ring size 4
135 >= 1 unsaturated non-aromatic heteroatom-containing ring size 4
136 >= 2 any ring size 4
137 >= 2 saturated or aromatic carbon-only ring size 4
138 >= 2 saturated or aromatic nitrogen-containing ring size 4
139 >= 2 saturated or aromatic heteroatom-containing ring size 4
140 >= 2 unsaturated non-aromatic carbon-only ring size 4
141 >= 2 unsaturated non-aromatic nitrogen-containing ring size 4
142 >= 2 unsaturated non-aromatic heteroatom-containing ring size 4

143 >= 1 any ring size 5

144 >= 1 saturated or aromatic carbon-only ring size 5
145 >= 1 saturated or aromatic nitrogen-containing ring size 5
146 >= 1 saturated or aromatic heteroatom-containing ring size 5
147 >= 1 unsaturated non-aromatic carbon-only ring size 5
148 >= 1 unsaturated non-aromatic nitrogen-containing ring size 5
149 >= 1 unsaturated non-aromatic heteroatom-containing ring size 5
150 >= 2 any ring size 5
151 >= 2 saturated or aromatic carbon-only ring size 5
152 >= 2 saturated or aromatic nitrogen-containing ring size 5
153 >= 2 saturated or aromatic heteroatom-containing ring size 5
154 >= 2 unsaturated non-aromatic carbon-only ring size 5
155 >= 2 unsaturated non-aromatic nitrogen-containing ring size 5
156 >= 2 unsaturated non-aromatic heteroatom-containing ring size 5
157 >= 3 any ring size 5
158 >= 3 saturated or aromatic carbon-only ring size 5
159 >= 3 saturated or aromatic nitrogen-containing ring size 5
160 >= 3 saturated or aromatic heteroatom-containing ring size 5
161 >= 3 unsaturated non-aromatic carbon-only ring size 5
162 >= 3 unsaturated non-aromatic nitrogen-containing ring size 5
163 >= 3 unsaturated non-aromatic heteroatom-containing ring size 5
164 >= 4 any ring size 5
165 >= 4 saturated or aromatic carbon-only ring size 5
166 >= 4 saturated or aromatic nitrogen-containing ring size 5
167 >= 4 saturated or aromatic heteroatom-containing ring size 5
168 >= 4 unsaturated non-aromatic carbon-only ring size 5
169 >= 4 unsaturated non-aromatic nitrogen-containing ring size 5
170 >= 4 unsaturated non-aromatic heteroatom-containing ring size 5
171 >= 5 any ring size 5
172 >= 5 saturated or aromatic carbon-only ring size 5
173 >= 5 saturated or aromatic nitrogen-containing ring size 5
174 >= 5 saturated or aromatic heteroatom-containing ring size 5
175 >= 5 unsaturated non-aromatic carbon-only ring size 5
176 >= 5 unsaturated non-aromatic nitrogen-containing ring size 5
177 >= 5 unsaturated non-aromatic heteroatom-containing ring size 5

178 >= 1 any ring size 6

179 >= 1 saturated or aromatic carbon-only ring size 6
180 >= 1 saturated or aromatic nitrogen-containing ring size 6
181 >= 1 saturated or aromatic heteroatom-containing ring size 6
182 >= 1 unsaturated non-aromatic carbon-only ring size 6

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PubChem Substructure Fingerprint Description (cont.)

Section 2: Rings in a canonic ESSR ring set (cont.)
Bit Position Bit Substructure
183 >= 1 unsaturated non-aromatic nitrogen-containing ring size 6
184 >= 1 unsaturated non-aromatic heteroatom-containing ring size 6
185 >= 2 any ring size 6
186 >= 2 saturated or aromatic carbon-only ring size 6
187 >= 2 saturated or aromatic nitrogen-containing ring size 6
188 >= 2 saturated or aromatic heteroatom-containing ring size 6
189 >= 2 unsaturated non-aromatic carbon-only ring size 6
190 >= 2 unsaturated non-aromatic nitrogen-containing ring size 6
191 >= 2 unsaturated non-aromatic heteroatom-containing ring size 6
192 >= 3 any ring size 6
193 >= 3 saturated or aromatic carbon-only ring size 6
194 >= 3 saturated or aromatic nitrogen-containing ring size 6
195 >= 3 saturated or aromatic heteroatom-containing ring size 6
196 >= 3 unsaturated non-aromatic carbon-only ring size 6
197 >= 3 unsaturated non-aromatic nitrogen-containing ring size 6
198 >= 3 unsaturated non-aromatic heteroatom-containing ring size 6
199 >= 4 any ring size 6
200 >= 4 saturated or aromatic carbon-only ring size 6
201 >= 4 saturated or aromatic nitrogen-containing ring size 6
202 >= 4 saturated or aromatic heteroatom-containing ring size 6
203 >= 4 unsaturated non-aromatic carbon-only ring size 6
204 >= 4 unsaturated non-aromatic nitrogen-containing ring size 6
205 >= 4 unsaturated non-aromatic heteroatom-containing ring size 6
206 >= 5 any ring size 6
207 >= 5 saturated or aromatic carbon-only ring size 6
208 >= 5 saturated or aromatic nitrogen-containing ring size 6
209 >= 5 saturated or aromatic heteroatom-containing ring size 6
210 >= 5 unsaturated non-aromatic carbon-only ring size 6
211 >= 5 unsaturated non-aromatic nitrogen-containing ring size 6
212 >= 5 unsaturated non-aromatic heteroatom-containing ring size 6

213 >= 1 any ring size 7

214 >= 1 saturated or aromatic carbon-only ring size 7
215 >= 1 saturated or aromatic nitrogen-containing ring size 7
216 >= 1 saturated or aromatic heteroatom-containing ring size 7
217 >= 1 unsaturated non-aromatic carbon-only ring size 7
218 >= 1 unsaturated non-aromatic nitrogen-containing ring size 7
219 >= 1 unsaturated non-aromatic heteroatom-containing ring size 7
220 >= 2 any ring size 7
221 >= 2 saturated or aromatic carbon-only ring size 7
222 >= 2 saturated or aromatic nitrogen-containing ring size 7
223 >= 2 saturated or aromatic heteroatom-containing ring size 7
224 >= 2 unsaturated non-aromatic carbon-only ring size 7
225 >= 2 unsaturated non-aromatic nitrogen-containing ring size 7
226 >= 2 unsaturated non-aromatic heteroatom-containing ring size 7

227 >= 1 any ring size 8

228 >= 1 saturated or aromatic carbon-only ring size 8
229 >= 1 saturated or aromatic nitrogen-containing ring size 8
230 >= 1 saturated or aromatic heteroatom-containing ring size 8
231 >= 1 unsaturated non-aromatic carbon-only ring size 8

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PubChem Substructure Fingerprint Description (cont.)

Section 2: Rings in a canonic ESSR ring set (cont.)
Bit Position Bit Substructure
232 >= 1 unsaturated non-aromatic nitrogen-containing ring size 8
233 >= 1 unsaturated non-aromatic heteroatom-containing ring size 8
234 >= 2 any ring size 8
235 >= 2 saturated or aromatic carbon-only ring size 8
236 >= 2 saturated or aromatic nitrogen-containing ring size 8
237 >= 2 saturated or aromatic heteroatom-containing ring size 8
238 >= 2 unsaturated non-aromatic carbon-only ring size 8
239 >= 2 unsaturated non-aromatic nitrogen-containing ring size 8
240 >= 2 unsaturated non-aromatic heteroatom-containing ring size 8

241 >= 1 any ring size 9

242 >= 1 saturated or aromatic carbon-only ring size 9
243 >= 1 saturated or aromatic nitrogen-containing ring size 9
244 >= 1 saturated or aromatic heteroatom-containing ring size 9
245 >= 1 unsaturated non-aromatic carbon-only ring size 9
246 >= 1 unsaturated non-aromatic nitrogen-containing ring size 9
247 >= 1 unsaturated non-aromatic heteroatom-containing ring size 9

248 >= 1 any ring size 10

249 >= 1 saturated or aromatic carbon-only ring size 10
250 >= 1 saturated or aromatic nitrogen-containing ring size 10
251 >= 1 saturated or aromatic heteroatom-containing ring size 10
252 >= 1 unsaturated non-aromatic carbon-only ring size 10
253 >= 1 unsaturated non-aromatic nitrogen-containing ring size 10
254 >= 1 unsaturated non-aromatic heteroatom-containing ring size 10

255 >= 1 aromatic ring

256 >= 1 hetero-aromatic ring
257 >= 2 aromatic rings
258 >= 2 hetero-aromatic rings
259 >= 3 aromatic rings
260 >= 3 hetero-aromatic rings
261 >= 4 aromatic rings
262 >= 4 hetero-aromatic rings

Section 3: Simple atom pairs – These bits test for the presence of
patterns of bonded atom pairs, regardless of bond order or
count.
Bit Position Bit Substructure
263 Li-H
264 Li-Li
265 Li-B
266 Li-C
267 Li-O
268 Li-F
269 Li-P
270 Li-S

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PubChem Substructure Fingerprint Description (cont.)

Section 3: Simple atom pairs (cont.)
Bit Position Bit Substructure
271 Li-Cl
272 B-H
273 B-B
274 B-C
275 B-N
276 B-O
277 B-F
278 B-Si
279 B-P
280 B-S
281 B-Cl
282 B-Br
283 C-H
284 C-C
285 C-N
286 C-O
287 C-F
288 C-Na
289 C-Mg
290 C-Al
291 C-Si
292 C-P
293 C-S
294 C-Cl
295 C-As
296 C-Se
297 C-Br
298 C-I
299 N-H
300 N-N
301 N-O
302 N-F
303 N-Si
304 N-P
305 N-S
306 N-Cl
307 N-Br
308 O-H
309 O-O
310 O-Mg
311 O-Na
312 O-Al
313 O-Si
314 O-P
315 O-K
316 F-P
317 F-S
318 Al-H
319 Al-Cl
320 Si-H

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PubChem Substructure Fingerprint Description (cont.)

Section 3: Simple atom pairs (cont.)
Bit Position Bit Substructure
321 Si-Si
322 Si-Cl
323 P-H
324 P-P
325 As-H
326 As-As

Section 4: Simple atom nearest neighbors – These bits test for the
presence of atom nearest neighbor patterns, regardless of
bond order (denoted by "~") or count, but where bond
aromaticity (denoted by ":") is significant.
Bit Position Bit Substructure
327 C(~Br)(~C)
328 C(~Br)(~C)(~C)
329 C(~Br)(~H)
330 C(~Br)(:C)
331 C(~Br)(:N)
332 C(~C)(~C)
333 C(~C)(~C)(~C)
334 C(~C)(~C)(~C)(~C)
335 C(~C)(~C)(~C)(~H)
336 C(~C)(~C)(~C)(~N)
337 C(~C)(~C)(~C)(~O)
338 C(~C)(~C)(~H)(~N)
339 C(~C)(~C)(~H)(~O)
340 C(~C)(~C)(~N)
341 C(~C)(~C)(~O)
342 C(~C)(~Cl)
343 C(~C)(~Cl)(~H)
344 C(~C)(~H)
345 C(~C)(~H)(~N)
346 C(~C)(~H)(~O)
347 C(~C)(~H)(~O)(~O)
348 C(~C)(~H)(~P)
349 C(~C)(~H)(~S)
350 C(~C)(~I)
351 C(~C)(~N)
352 C(~C)(~O)
353 C(~C)(~S)
354 C(~C)(~Si)
355 C(~C)(:C)
356 C(~C)(:C)(:C)
357 C(~C)(:C)(:N)
358 C(~C)(:N)
359 C(~C)(:N)(:N)
360 C(~Cl)(~Cl)

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PubChem Substructure Fingerprint Description (cont.)

Section 4: Simple atom nearest neighbors (cont.)
Bit Position Bit Substructure
361 C(~Cl)(~H)
362 C(~Cl)(:C)
363 C(~F)(~F)
364 C(~F)(:C)
365 C(~H)(~N)
366 C(~H)(~O)
367 C(~H)(~O)(~O)
368 C(~H)(~S)
369 C(~H)(~Si)
370 C(~H)(:C)
371 C(~H)(:C)(:C)
372 C(~H)(:C)(:N)
373 C(~H)(:N)
374 C(~H)(~H)(~H)
375 C(~N)(~N)
376 C(~N)(:C)
377 C(~N)(:C)(:C)
378 C(~N)(:C)(:N)
379 C(~N)(:N)
380 C(~O)(~O)
381 C(~O)(:C)
382 C(~O)(:C)(:C)
383 C(~S)(:C)
384 C(:C)(:C)
385 C(:C)(:C)(:C)
386 C(:C)(:C)(:N)
387 C(:C)(:N)
388 C(:C)(:N)(:N)
389 C(:N)(:N)
390 N(~C)(~C)
391 N(~C)(~C)(~C)
392 N(~C)(~C)(~H)
393 N(~C)(~H)
394 N(~C)(~H)(~N)
395 N(~C)(~O)
396 N(~C)(:C)
397 N(~C)(:C)(:C)
398 N(~H)(~N)
399 N(~H)(:C)
400 N(~H)(:C)(:C)
401 N(~O)(~O)
402 N(~O)(:O)
403 N(:C)(:C)
404 N(:C)(:C)(:C)
405 O(~C)(~C)
406 O(~C)(~H)
407 O(~C)(~P)
408 O(~H)(~S)
409 O(:C)(:C)
410 P(~C)(~C)

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PubChem Substructure Fingerprint Description (cont.)

Section 4: Simple atom nearest neighbors (cont.)
Bit Position Bit Substructure
411 P(~O)(~O)
412 S(~C)(~C)
413 S(~C)(~H)
414 S(~C)(~O)
415 Si(~C)(~C)

Section 5: Detailed atom neighborhoods – These bits test for the

presence of detailed atom neighborhood patterns, regardless
of count, but where bond orders are specific, bond
aromaticity matches both single and double bonds, and where
"-", "=", and "#" matches a single bond, double bond, and
triple bond order, respectively.
Bit Position Bit Substructure
416 C=C
417 C#C
418 C=N
419 C#N
420 C=O
421 C=S
422 N=N
423 N=O
424 N=P
425 P=O
426 P=P
427 C(#C)(-C)
428 C(#C)(-H)
429 C(#N)(-C)
430 C(-C)(-C)(=C)
431 C(-C)(-C)(=N)
432 C(-C)(-C)(=O)
433 C(-C)(-Cl)(=O)
434 C(-C)(-H)(=C)
435 C(-C)(-H)(=N)
436 C(-C)(-H)(=O)
437 C(-C)(-N)(=C)
438 C(-C)(-N)(=N)
439 C(-C)(-N)(=O)
440 C(-C)(-O)(=O)
441 C(-C)(=C)
442 C(-C)(=N)
443 C(-C)(=O)
444 C(-Cl)(=O)
445 C(-H)(-N)(=C)
446 C(-H)(=C)
447 C(-H)(=N)
448 C(-H)(=O)

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PubChem Substructure Fingerprint Description (cont.)

Section 5: Detailed atom neighborhoods (cont.)
Bit Position Bit Substructure
449 C(-N)(=C)
450 C(-N)(=N)
451 C(-N)(=O)
452 C(-O)(=O)
453 N(-C)(=C)
454 N(-C)(=O)
455 N(-O)(=O)
456 P(-O)(=O)
457 S(-C)(=O)
458 S(-O)(=O)
459 S(=O)(=O)

Section 6: Simple SMARTS patterns – These bits test for the presence
of simple SMARTS patterns, regardless of count, but where
bond orders are specific and bond aromaticity matches both
single and double bonds.
Bit Position Bit Substructure
460 C-C-C#C
461 O-C-C=N
462 O-C-C=O
463 N:C-S-[#1]
464 N-C-C=C
465 O=S-C-C
466 N#C-C=C
467 C=N-N-C
468 O=S-C-N
469 S-S-C:C
470 C:C-C=C
471 S:C:C:C
472 C:N:C-C
473 S-C:N:C
474 S:C:C:N
475 S-C=N-C
476 C-O-C=C
477 N-N-C:C
478 S-C=N-[#1]
479 S-C-S-C
480 C:S:C-C
481 O-S-C:C
482 C:N-C:C
483 N-S-C:C
484 N-C:N:C
485 N:C:C:N
486 N-C:N:N
487 N-C=N-C
488 N-C=N-[#1]

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PubChem Substructure Fingerprint Description (cont.)

Section 6: Simple SMARTS patterns (cont.)
Bit Position Bit Substructure
489 N-C-S-C
490 C-C-C=C
491 C-N:C-[#1]
492 N-C:O:C
493 O=C-C:C
494 O=C-C:N
495 C-N-C:C
496 N:N-C-[#1]
497 O-C:C:N
498 O-C=C-C
499 N-C:C:N
500 C-S-C:C
501 Cl-C:C-C
502 N-C=C-[#1]
503 Cl-C:C-[#1]
504 N:C:N-C
505 Cl-C:C-O
506 C-C:N:C
507 C-C-S-C
508 S=C-N-C
509 Br-C:C-C
510 [#1]-N-N-[#1]
511 S=C-N-[#1]
512 C-[As]-O-[#1]
513 S:C:C-[#1]
514 O-N-C-C
515 N-N-C-C
516 [#1]-C=C-[#1]
517 N-N-C-N
518 O=C-N-N
519 N=C-N-C
520 C=C-C:C
521 C:N-C-[#1]
522 C-N-N-[#1]
523 N:C:C-C
524 C-C=C-C
525 [As]-C:C-[#1]
526 Cl-C:C-Cl
527 C:C:N-[#1]
528 [#1]-N-C-[#1]
529 Cl-C-C-Cl
530 N:C-C:C
531 S-C:C-C
532 S-C:C-[#1]
533 S-C:C-N
534 S-C:C-O
535 O=C-C-C
536 O=C-C-N
537 O=C-C-O
538 N=C-C-C

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PubChem Substructure Fingerprint Description (cont.)

Section 6: Simple SMARTS patterns (cont.)
Bit Position Bit Substructure
539 N=C-C-[#1]
540 C-N-C-[#1]
541 O-C:C-C
542 O-C:C-[#1]
543 O-C:C-N
544 O-C:C-O
545 N-C:C-C
546 N-C:C-[#1]
547 N-C:C-N
548 O-C-C:C
549 N-C-C:C
550 Cl-C-C-C
551 Cl-C-C-O
552 C:C-C:C
553 O=C-C=C
554 Br-C-C-C
555 N=C-C=C
556 C=C-C-C
557 N:C-O-[#1]
558 O=N-C:C
559 O-C-N-[#1]
560 N-C-N-C
561 Cl-C-C=O
562 Br-C-C=O
563 O-C-O-C
564 C=C-C=C
565 C:C-O-C
566 O-C-C-N
567 O-C-C-O
568 N#C-C-C
569 N-C-C-N
570 C:C-C-C
571 [#1]-C-O-[#1]
572 N:C:N:C
573 O-C-C=C
574 O-C-C:C-C
575 O-C-C:C-O
576 N=C-C:C-[#1]
577 C:C-N-C:C
578 C-C:C-C:C
579 O=C-C-C-C
580 O=C-C-C-N
581 O=C-C-C-O
582 C-C-C-C-C
583 Cl-C:C-O-C
584 C:C-C=C-C
585 C-C:C-N-C
586 C-S-C-C-C
587 N-C:C-O-[#1]
588 O=C-C-C=O

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PubChem Substructure Fingerprint Description (cont.)

Section 6: Simple SMARTS patterns (cont.)
Bit Position Bit Substructure
589 C-C:C-O-C
590 C-C:C-O-[#1]
591 Cl-C-C-C-C
592 N-C-C-C-C
593 N-C-C-C-N
594 C-O-C-C=C
595 C:C-C-C-C
596 N=C-N-C-C
597 O=C-C-C:C
598 Cl-C:C:C-C
599 [#1]-C-C=C-[#1]
600 N-C:C:C-C
601 N-C:C:C-N
602 O=C-C-N-C
603 C-C:C:C-C
604 C-O-C-C:C
605 O=C-C-O-C
606 O-C:C-C-C
607 N-C-C-C:C
608 C-C-C-C:C
609 Cl-C-C-N-C
610 C-O-C-O-C
611 N-C-C-N-C
612 N-C-O-C-C
613 C-N-C-C-C
614 C-C-O-C-C
615 N-C-C-O-C
616 C:C:N:N:C
617 C-C-C-O-[#1]
618 C:C-C-C:C
619 O-C-C=C-C
620 C:C-O-C-C
621 N-C:C:C:N
622 O=C-O-C:C
623 O=C-C:C-C
624 O=C-C:C-N
625 O=C-C:C-O
626 C-O-C:C-C
627 O=[As]-C:C:C
628 C-N-C-C:C
629 S-C:C:C-N
630 O-C:C-O-C
631 O-C:C-O-[#1]
632 C-C-O-C:C
633 N-C-C:C-C
634 C-C-C:C-C
635 N-N-C-N-[#1]
636 C-N-C-N-C
637 O-C-C-C-C
638 O-C-C-C-N

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PubChem Substructure Fingerprint Description (cont.)

Section 6: Simple SMARTS patterns (cont.)
Bit Position Bit Substructure
639 O-C-C-C-O
640 C=C-C-C-C
641 O-C-C-C=C
642 O-C-C-C=O
643 [#1]-C-C-N-[#1]
644 C-C=N-N-C
645 O=C-N-C-C
646 O=C-N-C-[#1]
647 O=C-N-C-N
648 O=N-C:C-N
649 O=N-C:C-O
650 O=C-N-C=O
651 O-C:C:C-C
652 O-C:C:C-N
653 O-C:C:C-O
654 N-C-N-C-C
655 O-C-C-C:C
656 C-C-N-C-C
657 C-N-C:C-C
658 C-C-S-C-C
659 O-C-C-N-C
660 C-C=C-C-C
661 O-C-O-C-C
662 O-C-C-O-C
663 O-C-C-O-[#1]
664 C-C=C-C=C
665 N-C:C-C-C
666 C=C-C-O-C
667 C=C-C-O-[#1]
668 C-C:C-C-C
669 Cl-C:C-C=O
670 Br-C:C:C-C
671 O=C-C=C-C
672 O=C-C=C-[#1]
673 O=C-C=C-N
674 N-C-N-C:C
675 Br-C-C-C:C
676 N#C-C-C-C
677 C-C=C-C:C
678 C-C-C=C-C
679 C-C-C-C-C-C
680 O-C-C-C-C-C
681 O-C-C-C-C-O
682 O-C-C-C-C-N
683 N-C-C-C-C-C
684 O=C-C-C-C-C
685 O=C-C-C-C-N
686 O=C-C-C-C-O
687 O=C-C-C-C=O
688 C-C-C-C-C-C-C

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PubChem Substructure Fingerprint Description (cont.)

Section 6: Simple SMARTS patterns (cont.)
Bit Position Bit Substructure
689 O-C-C-C-C-C-C
690 O-C-C-C-C-C-O
691 O-C-C-C-C-C-N
692 O=C-C-C-C-C-C
693 O=C-C-C-C-C-O
694 O=C-C-C-C-C=O
695 O=C-C-C-C-C-N
696 C-C-C-C-C-C-C-C
697 C-C-C-C-C-C(C)-C
698 O-C-C-C-C-C-C-C
699 O-C-C-C-C-C(C)-C
700 O-C-C-C-C-C-O-C
701 O-C-C-C-C-C(O)-C
702 O-C-C-C-C-C-N-C
703 O-C-C-C-C-C(N)-C
704 O=C-C-C-C-C-C-C
705 O=C-C-C-C-C(O)-C
706 O=C-C-C-C-C(=O)-C
707 O=C-C-C-C-C(N)-C
708 C-C(C)-C-C
709 C-C(C)-C-C-C
710 C-C-C(C)-C-C
711 C-C(C)(C)-C-C
712 C-C(C)-C(C)-C

Section 7: Complex SMARTS patterns – These bits test for the presence
of complex SMARTS patterns, regardless of count, but where
bond orders and bond aromaticity are specific.
Bit Position Bit Substructure
713 Cc1ccc(C)cc1
714 Cc1ccc(O)cc1
715 Cc1ccc(S)cc1
716 Cc1ccc(N)cc1
717 Cc1ccc(Cl)cc1
718 Cc1ccc(Br)cc1
719 Oc1ccc(O)cc1
720 Oc1ccc(S)cc1
721 Oc1ccc(N)cc1
722 Oc1ccc(Cl)cc1
723 Oc1ccc(Br)cc1
724 Sc1ccc(S)cc1
725 Sc1ccc(N)cc1
726 Sc1ccc(Cl)cc1
727 Sc1ccc(Br)cc1
728 Nc1ccc(N)cc1
729 Nc1ccc(Cl)cc1
730 Nc1ccc(Br)cc1

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PubChem Substructure Fingerprint Description (cont.)

Section 7: Complex SMARTS patterns (cont.)
Bit Position Bit Substructure
731 Clc1ccc(Cl)cc1
732 Clc1ccc(Br)cc1
733 Brc1ccc(Br)cc1
734 Cc1cc(C)ccc1
735 Cc1cc(O)ccc1
736 Cc1cc(S)ccc1
737 Cc1cc(N)ccc1
738 Cc1cc(Cl)ccc1
739 Cc1cc(Br)ccc1
740 Oc1cc(O)ccc1
741 Oc1cc(S)ccc1
742 Oc1cc(N)ccc1
743 Oc1cc(Cl)ccc1
744 Oc1cc(Br)ccc1
745 Sc1cc(S)ccc1
746 Sc1cc(N)ccc1
747 Sc1cc(Cl)ccc1
748 Sc1cc(Br)ccc1
749 Nc1cc(N)ccc1
750 Nc1cc(Cl)ccc1
751 Nc1cc(Br)ccc1
752 Clc1cc(Cl)ccc1
753 Clc1cc(Br)ccc1
754 Brc1cc(Br)ccc1
755 Cc1c(C)cccc1
756 Cc1c(O)cccc1
757 Cc1c(S)cccc1
758 Cc1c(N)cccc1
759 Cc1c(Cl)cccc1
760 Cc1c(Br)cccc1
761 Oc1c(O)cccc1
762 Oc1c(S)cccc1
763 Oc1c(N)cccc1
764 Oc1c(Cl)cccc1
765 Oc1c(Br)cccc1
766 Sc1c(S)cccc1
767 Sc1c(N)cccc1
768 Sc1c(Cl)cccc1
769 Sc1c(Br)cccc1
770 Nc1c(N)cccc1
771 Nc1c(Cl)cccc1
772 Nc1c(Br)cccc1
773 Clc1c(Cl)cccc1
774 Clc1c(Br)cccc1
775 Brc1c(Br)cccc1
776 CC1CCC(C)CC1
777 CC1CCC(O)CC1
778 CC1CCC(S)CC1
779 CC1CCC(N)CC1
780 CC1CCC(Cl)CC1

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PubChem Substructure Fingerprint Description (cont.)

Section 7: Complex SMARTS patterns (cont.)
Bit Position Bit Substructure
781 CC1CCC(Br)CC1
782 OC1CCC(O)CC1
783 OC1CCC(S)CC1
784 OC1CCC(N)CC1
785 OC1CCC(Cl)CC1
786 OC1CCC(Br)CC1
787 SC1CCC(S)CC1
788 SC1CCC(N)CC1
789 SC1CCC(Cl)CC1
790 SC1CCC(Br)CC1
791 NC1CCC(N)CC1
792 NC1CCC(Cl)CC1
793 NC1CCC(Br)CC1
794 ClC1CCC(Cl)CC1
795 ClC1CCC(Br)CC1
796 BrC1CCC(Br)CC1
797 CC1CC(C)CCC1
798 CC1CC(O)CCC1
799 CC1CC(S)CCC1
800 CC1CC(N)CCC1
801 CC1CC(Cl)CCC1
802 CC1CC(Br)CCC1
803 OC1CC(O)CCC1
804 OC1CC(S)CCC1
805 OC1CC(N)CCC1
806 OC1CC(Cl)CCC1
807 OC1CC(Br)CCC1
808 SC1CC(S)CCC1
809 SC1CC(N)CCC1
810 SC1CC(Cl)CCC1
811 SC1CC(Br)CCC1
812 NC1CC(N)CCC1
813 NC1CC(Cl)CCC1
814 NC1CC(Br)CCC1
815 ClC1CC(Cl)CCC1
816 ClC1CC(Br)CCC1
817 BrC1CC(Br)CCC1
818 CC1C(C)CCCC1
819 CC1C(O)CCCC1
820 CC1C(S)CCCC1
821 CC1C(N)CCCC1
822 CC1C(Cl)CCCC1
823 CC1C(Br)CCCC1
824 OC1C(O)CCCC1
825 OC1C(S)CCCC1
826 OC1C(N)CCCC1
827 OC1C(Cl)CCCC1
828 OC1C(Br)CCCC1
829 SC1C(S)CCCC1
830 SC1C(N)CCCC1

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PubChem Substructure Fingerprint Description (cont.)

Section 7: Complex SMARTS patterns (cont.)
Bit Position Bit Substructure
831 SC1C(Cl)CCCC1
832 SC1C(Br)CCCC1
833 NC1C(N)CCCC1
834 NC1C(Cl)CCCC1
835 NC1C(Br)CCCC1
836 ClC1C(Cl)CCCC1
837 ClC1C(Br)CCCC1
838 BrC1C(Br)CCCC1
839 CC1CC(C)CC1
840 CC1CC(O)CC1
841 CC1CC(S)CC1
842 CC1CC(N)CC1
843 CC1CC(Cl)CC1
844 CC1CC(Br)CC1
845 OC1CC(O)CC1
846 OC1CC(S)CC1
847 OC1CC(N)CC1
848 OC1CC(Cl)CC1
849 OC1CC(Br)CC1
850 SC1CC(S)CC1
851 SC1CC(N)CC1
852 SC1CC(Cl)CC1
853 SC1CC(Br)CC1
854 NC1CC(N)CC1
855 NC1CC(Cl)CC1
856 NC1CC(Br)CC1
857 ClC1CC(Cl)CC1
858 ClC1CC(Br)CC1
859 BrC1CC(Br)CC1
860 CC1C(C)CCC1
861 CC1C(O)CCC1
862 CC1C(S)CCC1
863 CC1C(N)CCC1
864 CC1C(Cl)CCC1
865 CC1C(Br)CCC1
866 OC1C(O)CCC1
867 OC1C(S)CCC1
868 OC1C(N)CCC1
869 OC1C(Cl)CCC1
870 OC1C(Br)CCC1
871 SC1C(S)CCC1
872 SC1C(N)CCC1
873 SC1C(Cl)CCC1
874 SC1C(Br)CCC1
875 NC1C(N)CCC1
876 NC1C(Cl)CC1
877 NC1C(Br)CCC1
878 ClC1C(Cl)CCC1
879 ClC1C(Br)CCC1
880 BrC1C(Br)CCC1

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Decoding PubChem Fingerprints

PubChem fingerprints are currently 881 bits in length. Binary data is stored in
one byte increments. The fingerprint is, therefore, 111 bytes in length (888
bits), which includes padding of seven bits at the end to complete the last byte.
A four-byte prefix, containing the bit length of the fingerprint (881 bits),
increases the stored PubChem fingerprint size to 115 bytes (920 bits).

When PubChem fingerprints are encoded in base64 format, the base64-encoded

fingerprints are 156 bytes in length. The last two bytes are padding so that the
base64 length is divisible by four (156 bytes – 2 bytes = 154 bytes). Each base64
byte encodes six binary bits (154 bytes * 6 bits/byte = 924 bits). The last four
bits are padding to complete the last base64 byte (924 bits – 4 bits = 920 bits).
The resulting 920 binary bits (115 bytes) are described in the previous paragraph.

Document Version History

V1.3 – 2009May01 – Updated introduction to describe how to identify
the PubChem Substructure Fingerprint property in a
PubChem Compound record.
V1.2 – 2007Aug30 – Added section on decoding PubChem fingerprints.
V1.1 – 2007Aug06 – Corrected and expanded documentation of bits with
SMARTS patterns used.
V1.0 – 2005Dec02 - Initial release.

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