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 |
|---|---|---|---|
| 3dux | 64U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dux | 64U | Prothrombin | 3.4.21.5 | 1.000 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.858 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.825 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.818 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.810 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.788 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.775 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.775 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.773 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.769 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.755 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.755 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.752 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.749 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.739 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.737 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.727 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.725 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.723 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.712 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.707 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.703 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.698 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.691 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.689 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.689 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.685 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.681 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.677 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.670 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.663 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.663 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.663 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.662 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.660 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.657 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.657 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.652 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.651 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.648 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.645 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.645 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.644 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.643 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.642 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.637 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.635 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.634 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.634 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.631 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.628 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.625 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.624 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.618 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.617 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.612 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.610 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.609 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.608 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.608 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.607 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.604 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.598 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.593 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.591 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.591 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.590 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.590 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.588 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.588 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.585 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.577 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.577 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.577 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.575 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.575 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.572 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.572 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.568 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.560 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.553 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.549 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.548 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.548 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.545 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.532 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.522 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.516 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.514 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.509 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.508 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.507 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.504 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.502 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.500 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.495 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.491 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.489 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.484 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.480 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.480 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.480 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.476 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.472 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.466 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.465 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.462 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.460 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.460 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.460 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.459 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.459 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.458 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.458 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.456 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.456 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.455 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.454 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.452 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.451 | |
| 4h6p | FMN | Chromate reductase | / | 0.451 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3eks | CY9 | Actin-5C | / | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.446 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.446 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.446 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.446 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 2p2x | SAH | Diphthine synthase | / | 0.445 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.445 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.445 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.445 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.444 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 2p5c | SAH | Diphthine synthase | / | 0.443 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.442 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.442 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.441 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 3eku | CY9 | Actin-5C | / | 0.441 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.441 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.441 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.441 | |
| 4phl | PIL | Phosphodiesterase | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.440 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.440 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.440 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.440 | |
| 4e2b | FMN | Dehydrogenase | / | 0.440 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.440 |