sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2zfp | 19U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.804 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.787 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.771 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.757 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.745 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.740 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.739 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.723 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.718 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.711 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.709 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.702 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.701 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.699 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.696 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.695 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.690 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.690 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.687 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.683 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.675 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.671 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.670 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.669 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.669 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.668 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.663 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.660 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.653 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.652 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.651 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.650 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.649 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.648 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.645 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.644 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.642 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.638 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.638 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.637 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.635 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.632 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.630 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.628 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.627 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.626 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.625 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.625 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.623 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.623 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.622 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.621 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.620 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.620 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.619 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.619 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.616 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.615 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.615 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.614 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.613 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.610 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.608 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.604 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.599 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.599 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.598 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.596 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.593 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.589 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.588 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.587 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.586 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.585 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.583 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.581 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.578 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.578 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.574 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.566 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.564 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.561 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.556 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.555 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.551 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.551 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.548 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.547 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.546 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.545 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.545 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.543 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.540 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.540 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.530 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.521 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.519 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.513 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.512 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.512 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.510 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.503 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.498 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.496 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.495 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.491 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.481 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.479 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.478 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.475 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.473 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.469 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.469 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.468 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.466 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.465 | |
| 1fml | RTL | Retinol dehydratase | / | 0.464 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.464 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.464 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.463 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.462 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.462 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.461 | |
| 2p2x | SAH | Diphthine synthase | / | 0.460 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.460 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.459 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.459 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.458 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.457 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.457 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.456 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.456 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.455 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 5doz | NDP | JamJ | / | 0.455 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.454 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.454 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.453 | |
| 2ejk | SAH | Diphthine synthase | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.452 | |
| 4h6p | FMN | Chromate reductase | / | 0.452 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.451 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.450 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.450 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 2r8o | T5X | Transketolase 1 | / | 0.449 | |
| 3eks | CY9 | Actin-5C | / | 0.449 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.449 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.448 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.448 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.448 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.447 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.447 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.446 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.445 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.445 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 1o1t | 2NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.443 | |
| 2ele | SAH | Diphthine synthase | / | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2egb | SAH | Diphthine synthase | / | 0.442 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.442 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 2e7r | SAH | Diphthine synthase | / | 0.441 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.441 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.441 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.441 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.441 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.440 |