Table I.
The Number of Clusters Containing Patches (psize ≥200 Å2) and of Nonclustered Patches to Which SCOP Folds or CATH Topologies are Assigned, for the Top 20 Most Abundant Ligand IDs.
| Ligand name | # clusters (≥ 2 patches) to which SCOP are assigned | # patches to which SCOP is assigned, but not clustered | # SCOP fold assigned to the clusters | # clusters (≥ 2 patches) to which CATH are assigned | # patches to which CATH is assigned, but not clustered | # CATH topology assigned to the clusters | |
|---|---|---|---|---|---|---|---|
| ADP | Adenosine-5′-diphosphate | 91 (160) | 89 (171) | 32 | 102 (149) | 93 (167) | 44 |
| HEM | Protoporphyrin IX containing FE | 62 (86) | 140 (222) | 16 | 73 (75) | 166 (186) | 26 |
| FAD | Flavin-adenine dinucleotide | 21 (32) | 119 (238) | 11 | 22 (31) | 145 (212) | 18 |
| PLP | Pyridoxal-5′-phosphate | 49 (63) | 120 (187) | 7 | 48 (62) | 137 (170) | 10 |
| NAD | Nicotinamide-adenine-dinucleotide | 54 (78) | 98 (167) | 16 | 63 (69) | 130 (135) | 19 |
| ATP | Adenosine-5′-triphosphate | 49 (87) | 73 (134) | 29 | 53 (83) | 86 (121) | 31 |
| HEC | HEME C | 22 (36) | 105 (127) | 9 | 35 (23) | 111 (121) | 14 |
| FMN | Flavin Mononucleotide | 22 (41) | 58 (119) | 4 | 28 (35) | 81 (96) | 6 |
| GOL | Glycerol | 52 (119) | 15 (37) | 7 | 72 (99) | 26 (26) | 12 |
| NAP | NADP Nicotinamide-adenine-dinucleotide phosphate | 24 (45) | 60 (109) | 13 | 40 (29) | 85 (84) | 18 |
| ANP | Phosphoaminophosphonic acid-adenylate ester | 35 (66) | 46 (76) | 18 | 45 (56) | 45 (77) | 26 |
| AMP | Adenosine monophosphate | 36 (66) | 35 (58) | 13 | 48 (54) | 40 (53) | 15 |
| CL1 | Alpha chlorophyll A | 39 (45) | 70 (77) | 4 | 40 (44) | 70 (77) | 6 |
| GDP | Guanosine-5′-diphosphate | 31 (44) | 60 (74) | 11 | 33 (42) | 61 (74) | 15 |
| COA | Coenzyme A | 17 (28) | 58 (88) | 6 | 17 (28) | 55 (91) | 7 |
| NDP | NADPH Dihydro-nicotinamide-adenine-dinucleotide phosphate | 22 (30) | 54 (77) | 14 | 27 (25) | 59 (72) | 12 |
| SAH | S-Adenosyl-L-homocysteine | 29 (52) | 21 (48) | 5 | 32 (49) | 31 (38) | 11 |
| SAM | S-Adenosylmethionine | 23 (40) | 19 (44) | 5 | 21 (42) | 20 (43) | 7 |
| EPE | 4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acid | 35 (57) | 8 (21) | 2 | 41 (51) | 13 (16) | 4 |
| CIT | Citric acid | 20 (56) | 11 (18) | 5 | 37 (39) | 14 (15) | 6 |
The numbers in parentheses show the numbers of all clusters, including patches without SCCS.The symbol # indicates “the number of” CATH IDs were assigned to 20,250 patches for 7155 ligand IDs in the same way of SCOP (see details in Supporting Information 4). The high correlation, 0.96, between the number of SCOP fold assigned to clusters and that of CATH topology assigned to clusters was observed.