sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2zfp | 19U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.808 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.807 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.775 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.758 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.754 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.746 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.743 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.736 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.718 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.714 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.711 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.705 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.705 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.701 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.697 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.695 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.693 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.690 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.688 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.686 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.676 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.676 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.676 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.671 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.670 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.670 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.669 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.669 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.667 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.663 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.663 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.657 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.651 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.650 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.648 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.647 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.644 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.644 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.641 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.638 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.637 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.635 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.633 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.631 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.631 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.630 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.630 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.630 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.627 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.626 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.623 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.623 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.622 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.622 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.619 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.616 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.616 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.615 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.614 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.613 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.610 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.610 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.609 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.606 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.605 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.603 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.597 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.596 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.595 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.594 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.593 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.590 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2bvs | 2CE | 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 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.579 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.578 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.574 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.573 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.570 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.563 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.563 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.560 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.558 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.556 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.555 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.554 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.551 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.551 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.550 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.545 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.545 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.540 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.534 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.530 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.525 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.519 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.519 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.514 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.514 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.511 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.498 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.497 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.493 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.489 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.488 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.486 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.484 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.482 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.482 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.479 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.475 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.474 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.473 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.472 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.472 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.472 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.470 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.468 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.467 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.467 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.467 | |
| 5doz | NDP | JamJ | / | 0.467 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.466 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.465 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.464 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.464 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.464 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.462 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.462 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.459 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.459 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.458 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.458 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.456 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.455 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.455 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.454 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.454 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.453 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.452 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.452 | |
| 1c7o | PPG | Hemolysin | / | 0.451 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.450 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.450 | |
| 3eks | CY9 | Actin-5C | / | 0.450 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.450 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.450 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.450 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.449 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.449 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.448 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.448 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.448 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.447 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.447 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.447 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.446 | |
| 4e2d | FMN | Dehydrogenase | / | 0.446 | |
| 4h6p | FMN | Chromate reductase | / | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.445 | |
| 4hy0 | 1AQ | E3 ubiquitin-protein ligase XIAP | 6.3.2 | 0.445 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.445 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.444 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.444 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.444 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.444 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1o1t | 2NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.443 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.443 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.443 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.443 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.442 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.442 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.442 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.441 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.441 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.441 | |
| 2zre | AGS | Protein RecA | / | 0.441 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.441 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.441 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.441 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.440 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.440 |