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 |
|---|---|---|---|
| 2v3h | I25 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 1.000 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.699 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.699 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.691 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.685 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.684 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.683 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.679 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.679 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.678 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.675 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.662 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.661 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.660 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.657 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.654 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.651 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.650 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.647 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.647 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.644 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.641 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.638 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.637 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.634 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.633 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.632 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.632 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.628 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.627 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.627 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.625 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.622 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.621 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.621 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.620 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.620 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.615 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.615 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.613 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.613 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.613 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.613 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.610 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.610 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.609 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.608 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.608 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.604 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.601 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.601 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.600 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.599 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.599 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.598 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.597 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.597 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.597 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.596 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.593 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.592 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.590 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.590 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.590 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.589 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.586 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.585 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.582 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.580 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.580 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.580 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.579 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.578 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.574 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.573 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.573 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.571 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.565 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.563 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.563 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.558 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.557 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.557 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.555 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.555 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.553 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.553 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.548 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.547 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.540 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.534 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.533 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.530 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.528 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.522 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.517 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.516 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.507 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.503 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.500 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.496 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.495 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.490 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.488 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.484 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.481 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.480 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.479 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.478 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.475 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.474 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.473 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.472 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.468 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.468 | |
| 2nr4 | FMN | Conserved protein | / | 0.467 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.466 | |
| 4h6p | FMN | Chromate reductase | / | 0.465 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.461 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.459 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.458 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.454 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.453 | |
| 1o1t | 2NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.451 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3eku | CY9 | Actin-5C | / | 0.451 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.451 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.451 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.451 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.450 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.449 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.446 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.445 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 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 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.442 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.442 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |