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Table 2 Examples of named substructures and appearance in KEGG COMPOUND, KEGG DRUG and KNApSAcK databases.

From: KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics

KCF-S / annotation

COMPOUND

DRUG

KNApSAcK

 

#S / #C

#S / #C

#S / #C

BOND

   

C5a-N1b / amide bond

4174 / 2192

2678 / 1385

6784 / 2528

C7a-O7a / carboxylate ester bond

3040 / 2198

1787 / 1329

21857 / 13166

C5a-S2a / thioester bond

455 / 453

31 / 30

36 / 36

N2b-N2b / diazo bond

83 / 73

83 / 19

11 / 11

S3a-S3a / disulfide bond

40 / 37

40 / 26

43 / 33

N1b-N1b / hydrazine bond

15 / 13

22 / 15

3 / 3

TRIPLET

   

C6a-C1c-N1a / alpha-amino acid

512 / 484

113 / 104

191 / 183

C5a-C1b-C5a / beta-keto carbonyl

270 / 106

6 / 6

36 / 36

C6a-C5a-O5a / alpha-keto carboxylate

169 / 168

10 / 8

46 / 46

C6a-C1c-O1a / alpha-hydroxy carboxylate

167 / 154

236 / 137

108 / 87

VICINITY

   

C1y(C1y+C1y+O1a) / cyclic secondary alcohol

10099 / 3090

1171 / 388

49015 / 11697

C8y(C8x+C8x+O1a) / phenolic hydroxy

1562 / 1263

376 / 313

9978 / 7219

C5a(N1b+N1b+O5a) / pseudourea

66 / 65

82 / 77

46 / 43

N1c(C1b+C1b+C1b) / tertiary amine

54 / 48

302 / 235

0 / 0

C5x(N1x+N1x+O5x) / cyclic pseudourea

36 / 36

30 / 29

20 / 20

RING

   

C1y(C1b)-C1y(O1a)-C1y(O1a)-C1y(O1a)-C1y(O2a)-O2x / pyranose sugar ring

1024 / 824

64 / 54

7670 / 6187

C8x-N4y(C1y)-C8y(N5x)-C8y(C8y)-N5x / imidazole ring

549 / 535

48 / 47

84 / 84

C8x-N4y(C1y)-C8y-N5x-C8x-N5x-C8y(N1a)-C8y-N5x / adenine ring

428 / 420

17 / 17

55 / 55

C1x-C1x-N1y(C1b)-C1x-C1x-N1y(C1b) / piperazine ring

7 / 7

45 / 45

0 / 0

C8x-C8y(C2b)-C8x-C8y(O1a)-C8y(O1a)-C8y(O1a) / 5-alenylbenzene-1,2,3-triol

3 / 3

0 / 0

12 / 12

SKELETON

   

C1b(O2b)-C1y(O2x)-C1y(O1a)-C1y(O1a)-C1y(N4y+O2x) / ribofuranose

255 / 255

20 / 20

62 / 62

C1x(N1y)-C1x(N1y) / ethylenediamine in ring

136 / 136

702 / 702

0 / 0

C1a-C1c(C1a)-C1b-C1c(N1b)-C5a(N1b+O5a) / leucine residue

102 / 102

79 / 79

228 / 228

C7a(O6a+O7a)-C8y-C8x-C8x-C8y(O2a)-C8x-C8x / p-hydroxybenzoate residue

0 / 0

3 / 3

51 / 51

INORGANIC

   

O1c-P1b(O2b(C1y))(O1c)-O1c

520 / 520

19 / 19

66 / 66

/ cyclic secondary alcohol orthophosphate

   

O1c-P1b(O2b(C1b))(O1c)-O1c

387 / 387

43 / 43

97 / 97

/ primary alcohol orthophosphate

   

O1c-P1b(O2b(C1y))(O2b(C1b))-O1c / cyclic orthophosphate

173 / 173

2 / 2

2 / 2

O3a-N2b(C8y)-O3a / aryl nitro

304 / 304

164 / 164

48 / 48

N2b(C2c)-O1b / oxime

27 / 27

22 / 22

61 / 61

  1. #S represents the numbers of KCF-Substructures, and #C represent the numbers of compounds containing the KCF-Substructures. Note that the annotations are not necessary-and-sufficient definitions. For example, "N1b-N1b" bond is a hydrazine bond, but there are some other types of hydrazine bonds; e.g., "N1b-N1c" is a hydrazine bond with three substituted groups, and "N1x-N1x" is a hydrazine bond in a ring structure.