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 |
|---|---|---|---|
| 2zff | 53U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zff | 53U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.897 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.838 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.821 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.772 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.761 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.758 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.752 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.751 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.746 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.743 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.743 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.739 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.739 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.736 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.733 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.729 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.726 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.725 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.716 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.707 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.695 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.689 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.686 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.682 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.677 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.670 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.666 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.665 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.664 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.663 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.662 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.650 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.650 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.644 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.643 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.640 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.639 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.636 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.633 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.632 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.630 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.629 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.629 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.629 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.628 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.621 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.617 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.615 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.615 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.614 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.612 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.611 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.608 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.607 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.606 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.605 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.602 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.601 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.601 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.601 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.596 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.595 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.595 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.593 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.591 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.589 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.587 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.583 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.581 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.579 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.577 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.576 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.576 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.575 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.574 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.571 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.568 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.565 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.564 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.561 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.558 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.554 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.549 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.546 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.546 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.545 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.544 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.540 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.539 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.537 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.534 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.530 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.530 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.528 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.521 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.521 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.518 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.517 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.514 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.506 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.505 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.498 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.497 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.485 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.479 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.477 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.472 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.470 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.469 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.469 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.468 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.466 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.466 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.465 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.465 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.464 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.463 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 5doz | NDP | JamJ | / | 0.461 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.460 | |
| 2ehl | SAH | Diphthine synthase | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.459 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.459 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.458 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.458 | |
| 1fml | RTL | Retinol dehydratase | / | 0.457 | |
| 1wqv | PSM | Coagulation factor VII | 3.4.21.21 | 0.457 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.457 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.456 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3eku | CY9 | Actin-5C | / | 0.456 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.456 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.455 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.454 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.454 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 2ejz | SAH | Diphthine synthase | / | 0.453 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.453 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 2ejk | SAH | Diphthine synthase | / | 0.451 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.451 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.450 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.450 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.449 | |
| 1tl7 | ONM | Adenylate cyclase type 2 | / | 0.449 | |
| 1tl7 | ONM | Adenylate cyclase type 5 | / | 0.449 | |
| 2ele | SAH | Diphthine synthase | / | 0.449 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3eks | CY9 | Actin-5C | / | 0.449 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.449 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.448 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.448 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.448 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.448 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.447 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.447 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.446 | |
| 2p2x | SAH | Diphthine synthase | / | 0.446 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.446 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.446 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.445 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.444 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.444 | |
| 2wat | COA | Fatty acid synthase subunit alpha | 2.3.1.86 | 0.444 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.444 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.444 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.444 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.444 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.443 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2egb | SAH | Diphthine synthase | / | 0.443 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3au2 | DGT | DNA polymerase beta family (X family) | / | 0.443 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.443 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 1ohh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.442 | |
| 1ohh | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.442 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.442 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4fuj | 1U9 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.442 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3c1o | NAP | Eugenol synthase | / | 0.441 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.441 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.441 | |
| 4e2d | FMN | Dehydrogenase | / | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 1i3m | UD1 | UDP-glucose 4-epimerase | / | 0.440 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.440 | |
| 1t3z | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.440 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.440 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.440 |