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 |
|---|---|---|---|
| 3biu | 10U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3biu | 10U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.808 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.796 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.791 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.780 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.778 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.772 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.771 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.766 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.764 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.758 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.747 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.740 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.736 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.736 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.727 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.722 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.717 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.700 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.698 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.693 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.678 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.670 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.670 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.668 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.664 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.659 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.657 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.655 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.654 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.653 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.652 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.650 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.648 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.648 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.648 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.644 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.642 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.642 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.641 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.638 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.636 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.634 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.629 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.628 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.626 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.625 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.622 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.621 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.621 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.620 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.618 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.617 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.614 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.614 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.609 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.608 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.608 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.606 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.604 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.603 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.601 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.600 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.587 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.586 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.586 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.580 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.579 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.579 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.575 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.575 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.572 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.563 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.563 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.557 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.553 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.550 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.547 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.544 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.533 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.530 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.528 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.522 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.521 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.518 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.515 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.506 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.505 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.499 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.490 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.489 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.488 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.480 | |
| 4h6p | FMN | Chromate reductase | / | 0.480 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.476 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.475 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.470 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.462 | |
| 2c4f | GIL | Coagulation factor VII | 3.4.21.21 | 0.461 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.461 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.460 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.460 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.460 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.460 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.459 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.459 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.458 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.455 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.454 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.454 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.452 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.452 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.452 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.452 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.451 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.451 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.450 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.450 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3rdq | DTB | Streptavidin | / | 0.449 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.448 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.448 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.448 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.448 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.448 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.447 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.447 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.447 | |
| 3e8x | NAP | BH1520 protein | / | 0.446 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4ckr | DI1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.445 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.444 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.443 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.442 | |
| 1hf3 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.441 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.441 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.440 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.440 |