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 |
|---|---|---|---|
| 3kdb | 006 | Gag-Pol polyprotein | 3.4.23.16 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3kdb | 006 | Gag-Pol polyprotein | 3.4.23.16 | 1.000 | |
| 2nnk | ROC | Protease | / | 0.685 | |
| 3sa5 | A69 | Protease | / | 0.644 | |
| 1ec2 | BEJ | Gag-Pol polyprotein | 3.4.23.16 | 0.641 | |
| 2i4x | KGQ | Protease | / | 0.637 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 0.637 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.636 | |
| 3qn8 | NI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.633 | |
| 1w5x | BE5 | Gag-Pol polyprotein | 3.4.23.16 | 0.632 | |
| 3ok9 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.630 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.625 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.618 | |
| 1w5y | BE6 | Gag-Pol polyprotein | 3.4.23.16 | 0.613 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.613 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.612 | |
| 4njs | G08 | Protease | / | 0.612 | |
| 3sa3 | 23X | Protease | / | 0.610 | |
| 2qnn | QN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.609 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.607 | |
| 4heg | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.607 | |
| 3ndt | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.606 | |
| 4njt | 017 | Protease | / | 0.606 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.604 | |
| 3sa7 | 55A | Protease | / | 0.604 | |
| 3ndw | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.603 | |
| 3mxe | K54 | Gag-Pol polyprotein | 3.4.23.16 | 0.602 | |
| 4hdb | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.602 | |
| 1a9m | U0E | Gag-Pol polyprotein | / | 0.601 | |
| 1hsg | MK1 | Gag-Pol polyprotein | / | 0.601 | |
| 3o9c | K20 | Pol polyprotein | / | 0.601 | |
| 3o9f | K2D | Gag-Pol polyprotein | / | 0.601 | |
| 1dw6 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.599 | |
| 2pk5 | 075 | Protease | / | 0.597 | |
| 3hzc | 2NC | Protease | / | 0.597 | |
| 1dif | A85 | Gag-Pol polyprotein | / | 0.596 | |
| 1t3r | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.596 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.595 | |
| 3gga | GGW | Gag-Pol polyprotein | / | 0.594 | |
| 2hc0 | AB2 | Protease | / | 0.593 | |
| 2idw | 017 | Protease | / | 0.593 | |
| 1zsr | 0ZT | Gag-Pol polyprotein | 3.4.23.16 | 0.592 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.592 | |
| 1ec1 | BEE | Gag-Pol polyprotein | 3.4.23.16 | 0.591 | |
| 3k4v | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.588 | |
| 3pwm | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.588 | |
| 3qrs | NK8 | Gag-Pol polyprotein | 3.4.23.16 | 0.588 | |
| 3sa6 | F71 | Protease | / | 0.588 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.588 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.587 | |
| 3nxe | 2NC | Protease | / | 0.587 | |
| 3oxc | ROC | Protease | / | 0.587 | |
| 4hdf | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.587 | |
| 4kb9 | G79 | Protease | / | 0.587 | |
| 1n49 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.586 | |
| 2uy0 | HV1 | Gag-Pol polyprotein | 3.4.23.16 | 0.586 | |
| 3nyg | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.585 | |
| 3o9e | A60 | Pol polyprotein | / | 0.585 | |
| 1hxb | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.584 | |
| 3ndu | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.584 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.583 | |
| 2uxz | HI1 | Gag-Pol polyprotein | 3.4.23.16 | 0.582 | |
| 3qpj | N4I | Gag-Pol polyprotein | 3.4.23.16 | 0.582 | |
| 3zps | EQM | Gag-Pol polyprotein | 3.4.23.16 | 0.582 | |
| 2f3k | RO1 | Protease | / | 0.581 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.581 | |
| 2p3d | 3TL | Protease | / | 0.581 | |
| 1hvj | A78 | Gag-Pol polyprotein | / | 0.580 | |
| 1rl8 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.580 | |
| 1hos | PHP | Gag-Pol polyprotein | / | 0.579 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.579 | |
| 1wbm | BLL | Pol protein | / | 0.578 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.578 | |
| 3o9b | K2A | Pol polyprotein | / | 0.578 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.577 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.576 | |
| 2qi6 | MZ8 | Gag-Pol polyprotein | / | 0.573 | |
| 1vij | BAY | Gag-Pol polyprotein | / | 0.572 | |
| 2rkf | AB1 | Pol protein | / | 0.572 | |
| 1w5w | BE4 | Gag-Pol polyprotein | 3.4.23.16 | 0.571 | |
| 1yt9 | OIS | Gag-Pol polyprotein | / | 0.571 | |
| 2wkz | 5AH | Gag-Pol polyprotein | / | 0.571 | |
| 3ekp | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.571 | |
| 3s85 | LK0 | Gag-Pol polyprotein | / | 0.571 | |
| 3el5 | 1UN | Gag-Pol polyprotein | / | 0.570 | |
| 3kfs | 3TL | Gag-Pol polyprotein | / | 0.570 | |
| 1ec0 | BED | Gag-Pol polyprotein | 3.4.23.16 | 0.569 | |
| 1ffi | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.569 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.568 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.568 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.567 | |
| 1hvl | A76 | Gag-Pol polyprotein | / | 0.566 | |
| 2bpv | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.566 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.566 | |
| 3ckt | YDP | Gag-Pol polyprotein | 3.4.23.16 | 0.566 | |
| 2b60 | RIT | Pol polyprotein | / | 0.565 | |
| 2qhz | MZ2 | Gag-Pol polyprotein | / | 0.565 | |
| 4dqe | 017 | Gag-Pol polyprotein | / | 0.565 | |
| 1hvk | A79 | Gag-Pol polyprotein | / | 0.564 | |
| 2p3a | 3TL | Pol protein | / | 0.563 | |
| 3bva | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.563 | |
| 3s56 | ROC | Protease | / | 0.563 | |
| 1ebz | BEC | Gag-Pol polyprotein | 3.4.23.16 | 0.562 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.562 | |
| 1fg6 | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.561 | |
| 3ekq | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.561 | |
| 3ggx | GGX | Gag-Pol polyprotein | / | 0.560 | |
| 4a4q | UX9 | Pol protein | / | 0.560 | |
| 1hvi | A77 | Protease | / | 0.559 | |
| 1tcx | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.559 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.559 | |
| 2p3b | 3TL | V-1 protease | / | 0.559 | |
| 3gi6 | D78 | Gag-Pol polyprotein | / | 0.559 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.558 | |
| 2qi0 | MZ3 | Gag-Pol polyprotein | / | 0.557 | |
| 4djq | M86 | Pol polyprotein | / | 0.557 | |
| 3sa4 | F72 | Protease | / | 0.556 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.555 | |
| 2avs | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.554 | |
| 2hs2 | 017 | Protease | / | 0.554 | |
| 4djp | M73 | Pol polyprotein | / | 0.554 | |
| 4dqf | 017 | Gag-Pol polyprotein | / | 0.554 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.553 | |
| 4qgi | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.553 | |
| 3d20 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.551 | |
| 3em6 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.551 | |
| 3vf7 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.551 | |
| 3sab | F78 | Protease | / | 0.550 | |
| 1fgc | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.546 | |
| 3lit | E15 | Protease | / | 0.546 | |
| 1z1r | HBH | Gag-Pol polyprotein | 3.4.23.16 | 0.545 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.545 | |
| 3bhe | BZN | Gag-Pol polyprotein | 3.4.23.16 | 0.544 | |
| 3liq | E14 | Protease | / | 0.544 | |
| 3lin | E13 | Protease | / | 0.543 | |
| 3nu6 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.543 | |
| 2qhy | MZ1 | Gag-Pol polyprotein | / | 0.542 | |
| 3liv | E16 | Protease | / | 0.542 | |
| 3mws | 017 | Pol protein | / | 0.542 | |
| 3vfb | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.542 | |
| 1sdu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.539 | |
| 2a1e | IPF | Gag-Pol polyprotein | 3.4.23.16 | 0.539 | |
| 2fle | AI | Protease | / | 0.539 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.537 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.537 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.536 | |
| 1ivp | 1ZK | Gag-Pol polyprotein | / | 0.535 | |
| 1qbr | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.534 | |
| 3sac | AF8 | Protease | / | 0.533 | |
| 1meu | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.532 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.532 | |
| 3lzu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.531 | |
| 1odx | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.527 | |
| 3ekv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.527 | |
| 4q1w | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.527 | |
| 3qro | NK9 | Gag-Pol polyprotein | 3.4.23.16 | 0.525 | |
| 4q1y | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.525 | |
| 2i4u | DJR | Protease | / | 0.524 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.524 | |
| 2p3c | 3TL | Protease | / | 0.523 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.521 | |
| 2hs1 | 017 | Protease | / | 0.520 | |
| 2i0d | MUT | Protease | / | 0.520 | |
| 2psu | MUU | Protease | / | 0.520 | |
| 3ekx | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.520 | |
| 3lix | E17 | Protease | / | 0.520 | |
| 3o9h | K2E | Gag-Pol polyprotein | / | 0.520 | |
| 1d4l | PI9 | Gag-Pol polyprotein | 3.4.23.16 | 0.519 | |
| 2rkg | AB1 | Pol protein | / | 0.519 | |
| 1sh9 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.518 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.517 | |
| 4dqb | 017 | Gag-Pol polyprotein | / | 0.517 | |
| 2pwr | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.516 | |
| 3lzv | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.514 | |
| 1tcw | IM1 | Gag-Pol polyprotein | / | 0.513 | |
| 1a8k | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.512 | |
| 1qbt | 146 | Gag-Pol polyprotein | 3.4.23.16 | 0.512 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.510 | |
| 1a94 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.506 | |
| 1bdq | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.506 | |
| 3wsj | MK1 | Protease | / | 0.505 | |
| 1k2c | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.504 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.503 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.501 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.500 | |
| 4q1x | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.494 | |
| 3uhl | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.493 | |
| 1mrx | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.492 | |
| 1mer | DMQ | Gag-Pol polyprotein | 3.4.23.16 | 0.490 | |
| 2psv | MUV | Protease | / | 0.490 | |
| 2wl0 | 5AH | Gag-Pol polyprotein | / | 0.477 | |
| 1ivq | 0PX | Gag-Pol polyprotein | / | 0.476 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.473 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.465 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.464 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.463 | |
| 2bqv | A1A | Protease | / | 0.463 | |
| 3ecg | 065 | Gag-Pol polyprotein | 3.4.23.47 | 0.463 | |
| 4k4p | 3TL | Gag-Pol polyprotein | / | 0.462 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.460 | |
| 4ic7 | ANP | Mitogen-activated protein kinase 7 | 2.7.11.24 | 0.459 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.454 | |
| 2uzw | SS4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.449 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 4hi0 | GDP | Urease accessory protein UreG | / | 0.447 | |
| 2gnf | Y27 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3anx | MTA | Polyamine aminopropyltransferase | / | 0.445 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.445 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.444 | |
| 4g17 | 0VN | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.444 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 1ke6 | LS2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 4rcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.440 |