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 |
|---|---|---|---|
| 2uuj | 896 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 1.000 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.657 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.655 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.642 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.640 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.634 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.633 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.631 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.630 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.630 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.629 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.628 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.627 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.626 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.623 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.623 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.623 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.620 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.619 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.619 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.616 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.611 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.611 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.609 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.609 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.608 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.607 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.605 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.605 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.604 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.603 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.602 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.601 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.599 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.598 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.597 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.597 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.596 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.596 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.592 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.590 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.590 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.586 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.585 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.583 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.583 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.583 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.582 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.577 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.577 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.576 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.576 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.575 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.574 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.574 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.573 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.573 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.570 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.570 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.569 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.569 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.567 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.566 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.561 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.559 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.556 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.553 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.553 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.552 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.549 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.547 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.542 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.541 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.539 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.539 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.531 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.520 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.509 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.509 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.498 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.498 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.495 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.488 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.487 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.478 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.476 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.474 | |
| 4yfy | 0FX | VioF | / | 0.471 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.469 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.469 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.468 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.461 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.459 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1hf3 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.457 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.457 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.456 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.453 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.451 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3eks | CY9 | Actin-5C | / | 0.451 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 8dfr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.448 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.448 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.447 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.446 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.445 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.444 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4h6p | FMN | Chromate reductase | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.442 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3eku | CY9 | Actin-5C | / | 0.442 | |
| 3ndj | JHZ | Methyltransferase | / | 0.442 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.441 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.441 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.440 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.440 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.440 |