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 |
|---|---|---|---|
| 4bam | MM9 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 1.000 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.817 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.813 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.804 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.797 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.787 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.765 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.756 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.744 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.741 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.732 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.729 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.718 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.716 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.715 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.706 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.698 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.694 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.691 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.678 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.670 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.670 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.663 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.660 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.654 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.653 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.650 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.648 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.647 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.646 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.644 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.643 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.642 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.641 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.639 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.639 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.638 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.637 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.637 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.630 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.628 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.626 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.626 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.623 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.620 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.617 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.616 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.612 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.611 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.610 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.606 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.605 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.603 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.602 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.601 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.595 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.595 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.594 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.593 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.592 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.592 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.590 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.589 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.588 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.585 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.583 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.578 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.574 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.574 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.572 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.571 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.570 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.570 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.568 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.568 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.567 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.567 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.566 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.562 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.554 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.549 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.545 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.543 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.540 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.534 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.528 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.522 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.513 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.513 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.506 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.505 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.501 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.500 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.500 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.489 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.482 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.482 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.478 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.474 | |
| 2ele | SAH | Diphthine synthase | / | 0.472 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.472 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.469 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.469 | |
| 2dxx | SAH | Diphthine synthase | / | 0.465 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.463 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.463 | |
| 2e7r | SAH | Diphthine synthase | / | 0.462 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.462 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.461 | |
| 2ejk | SAH | Diphthine synthase | / | 0.460 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.459 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.458 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 2p6i | SAH | Diphthine synthase | / | 0.456 | |
| 2pcg | SAH | Diphthine synthase | / | 0.456 | |
| 3eku | CY9 | Actin-5C | / | 0.456 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.456 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.455 | |
| 2pch | SAH | Diphthine synthase | / | 0.455 | |
| 2pck | SAH | Diphthine synthase | / | 0.455 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.455 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
| 2e8r | SAH | Diphthine synthase | / | 0.453 | |
| 2eka | SAH | Diphthine synthase | / | 0.453 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4xr9 | NAD | CalS8 | / | 0.453 | |
| 2ehl | SAH | Diphthine synthase | / | 0.452 | |
| 2p5c | SAH | Diphthine synthase | / | 0.452 | |
| 4h6p | FMN | Chromate reductase | / | 0.452 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.451 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.451 | |
| 2owg | SAH | Diphthine synthase | / | 0.450 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.450 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.450 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.449 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.449 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.449 | |
| 2egb | SAH | Diphthine synthase | / | 0.449 | |
| 2emr | SAH | Diphthine synthase | / | 0.449 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.449 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.449 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.449 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.448 | |
| 2p2x | SAH | Diphthine synthase | / | 0.448 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.448 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.446 | |
| 2eni | SAH | Diphthine synthase | / | 0.446 | |
| 2pci | SAH | Diphthine synthase | / | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.446 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.446 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 2huv | SAH | Diphthine synthase | / | 0.445 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 2p5f | SAH | Diphthine synthase | / | 0.444 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.444 | |
| 2dsh | SAH | Diphthine synthase | / | 0.443 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.443 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2ejz | SAH | Diphthine synthase | / | 0.442 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.441 | |
| 3ntq | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.441 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.440 |