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 |
|---|---|---|---|
| 2zgx | 29U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.833 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.819 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.810 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.809 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.799 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.796 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.794 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.788 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.776 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.769 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.767 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.764 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.763 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.760 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.760 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.746 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.742 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.740 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.718 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.712 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.699 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.698 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.688 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.683 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.681 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.680 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.680 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.679 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.679 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.677 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.676 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.675 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.671 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.669 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.668 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.665 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.663 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.663 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.662 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.662 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.659 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.657 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.657 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.655 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.654 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.654 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.645 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.643 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.643 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.642 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.634 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.634 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.625 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.622 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.621 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.620 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.620 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.619 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.619 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.616 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.612 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.610 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.608 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.607 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.606 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.606 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.603 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.603 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.602 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.597 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.597 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.596 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.595 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.594 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.593 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.592 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.592 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.590 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.586 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.583 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.579 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.578 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.574 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.573 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.573 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.572 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.565 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.562 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.560 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.559 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.551 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.549 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.548 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.543 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.536 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.531 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.526 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.519 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.518 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.513 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.509 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.507 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.504 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.501 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.500 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.494 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.490 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.488 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.479 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.469 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.468 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.464 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.463 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.462 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.459 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.458 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.457 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.454 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.453 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.453 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.453 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.452 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.448 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.446 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.445 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3eku | CY9 | Actin-5C | / | 0.444 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.444 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.440 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.440 |