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 |
|---|---|---|---|
| 1mu8 | CDB | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 1.000 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.757 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.745 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.701 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.681 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.647 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.644 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.642 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.639 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.638 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.631 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.625 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.622 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.610 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.609 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.607 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.606 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.605 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.604 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.602 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.601 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.599 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.597 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.594 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.589 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.587 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.587 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.586 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.586 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.586 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.584 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.579 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.578 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.578 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.577 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.574 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.573 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.570 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.570 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.569 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.568 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.568 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.565 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.564 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.563 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.561 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.561 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.560 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.559 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.558 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.557 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.556 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.555 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.555 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.552 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.552 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.551 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.550 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.550 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.550 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.549 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.545 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.538 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.535 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.533 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.533 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.533 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.530 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.528 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.526 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.526 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.523 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.520 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.520 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.519 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.518 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.516 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.514 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.512 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.511 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.511 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.502 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.502 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.502 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.500 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.500 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.499 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.497 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.495 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.493 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.489 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.489 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.487 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.487 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.486 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.481 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.476 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.476 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.476 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.476 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.475 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.470 | |
| 1nt1 | T76 | Prothrombin | 3.4.21.5 | 0.468 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.468 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.468 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.467 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.465 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.464 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.464 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.461 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.459 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.458 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.457 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.457 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.452 | |
| 1owe | 675 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.452 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3v0x | ANH | Cationic trypsin | 3.4.21.4 | 0.451 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.450 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 2nr4 | FMN | Conserved protein | / | 0.448 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.447 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.446 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.443 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1iqg | XME | Coagulation factor X | 3.4.21.6 | 0.442 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.442 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.441 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.441 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1cne | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.440 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.440 |