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 |
|---|---|---|---|
| 3s85 | LK0 | Gag-Pol polyprotein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3s85 | LK0 | Gag-Pol polyprotein | / | 1.000 | |
| 4kb9 | G79 | Protease | / | 0.499 | |
| 3ggx | GGX | Gag-Pol polyprotein | / | 0.496 | |
| 1ec2 | BEJ | Gag-Pol polyprotein | 3.4.23.16 | 0.494 | |
| 2pk6 | O33 | V-1 protease | / | 0.493 | |
| 2pk5 | 075 | Protease | / | 0.489 | |
| 3a2o | KNJ | Gag-Pol polyprotein | 3.4.23.16 | 0.487 | |
| 1hvj | A78 | Gag-Pol polyprotein | / | 0.485 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.485 | |
| 3kdc | JZP | Gag-Pol polyprotein | 3.4.23.16 | 0.484 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.484 | |
| 3ndw | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.483 | |
| 2qd6 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.482 | |
| 2uy0 | HV1 | Gag-Pol polyprotein | 3.4.23.16 | 0.482 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.482 | |
| 2bqv | A1A | Protease | / | 0.481 | |
| 2xyf | G40 | Gag-Pol polyprotein | / | 0.481 | |
| 3el9 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.481 | |
| 4rvj | 478 | Protease | / | 0.481 | |
| 1ivp | 1ZK | Gag-Pol polyprotein | / | 0.480 | |
| 2cen | 4AH | Protease | / | 0.479 | |
| 1d4y | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.478 | |
| 1hvi | A77 | Protease | / | 0.478 | |
| 2aqu | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.478 | |
| 1vij | BAY | Gag-Pol polyprotein | / | 0.477 | |
| 2qnn | QN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.477 | |
| 2cem | 2AH | Pol protein | / | 0.475 | |
| 3gga | GGW | Gag-Pol polyprotein | / | 0.475 | |
| 2wkz | 5AH | Gag-Pol polyprotein | / | 0.474 | |
| 4djo | MK5 | Pol polyprotein | / | 0.474 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.473 | |
| 2ieo | 017 | Protease | / | 0.473 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.473 | |
| 2a4f | AAU | V-1 protease | / | 0.472 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.471 | |
| 2xye | CXG | Gag-Pol polyprotein | / | 0.471 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 4hdf | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 3ekp | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 3zps | EQM | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.468 | |
| 1wbk | 568 | Pol protein | / | 0.468 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 2qnp | QN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 3kf0 | 3TL | Gag-Pol polyprotein | / | 0.468 | |
| 3nu4 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 1tcx | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 2nmy | ROC | Protease | / | 0.467 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 3ndx | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 3ok9 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 4a4q | UX9 | Pol protein | / | 0.466 | |
| 2fdd | 385 | Pol protein | / | 0.465 | |
| 1fgc | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1hvs | A77 | Gag-Pol polyprotein | / | 0.464 | |
| 2bpv | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3k4v | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3ndt | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3ndu | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1dif | A85 | Gag-Pol polyprotein | / | 0.463 | |
| 1ebz | BEC | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 1w5y | BE6 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 3nu9 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 4nju | TPV | Protease | / | 0.463 | |
| 4njv | RIT | Protease | / | 0.463 | |
| 1ebw | BEI | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 2bpz | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 1npa | 3NH | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 1npw | LGZ | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 1w5x | BE5 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2bpy | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4ye3 | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2fxd | DR7 | Pol polyprotein | / | 0.460 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.460 | |
| 2p3b | 3TL | V-1 protease | / | 0.460 | |
| 3kfn | 3TL | Gag-Pol polyprotein | / | 0.460 | |
| 1hxw | RIT | Gag-Pol polyprotein | / | 0.459 | |
| 2aid | THK | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 2idw | 017 | Protease | / | 0.459 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 3em6 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 7upj | INU | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 2aoe | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 2i4w | KGQ | Protease | / | 0.457 | |
| 2qd8 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2uxz | HI1 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 3bxr | DRR | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 3bxs | DRS | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2a1e | IPF | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 2hb3 | GRL | Protease | / | 0.456 | |
| 3qn8 | NI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 3vfb | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 4hdb | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1a9m | U0E | Gag-Pol polyprotein | / | 0.455 | |
| 1ec0 | BED | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 1ffi | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 1sbg | IM1 | Gag-Pol polyprotein | / | 0.455 | |
| 2f8g | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3oxc | ROC | Protease | / | 0.455 | |
| 2wl0 | 5AH | Gag-Pol polyprotein | / | 0.454 | |
| 3hzc | 2NC | Protease | / | 0.454 | |
| 3nyg | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1d4i | BEG | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2hc0 | AB2 | Protease | / | 0.453 | |
| 2qhc | AB1 | Protease | / | 0.453 | |
| 3nxe | 2NC | Protease | / | 0.453 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1daz | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1hxb | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1k1u | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1dw6 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1ec1 | BEE | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1hpo | UNI | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1k2b | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3mxe | K54 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1rl8 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1z1h | HBB | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3nuo | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1hsg | MK1 | Gag-Pol polyprotein | / | 0.449 | |
| 2nnk | ROC | Protease | / | 0.449 | |
| 2p3d | 3TL | Protease | / | 0.449 | |
| 4djq | M86 | Pol polyprotein | / | 0.449 | |
| 4njs | G08 | Protease | / | 0.449 | |
| 3nls | 016 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3s43 | 478 | Protease | / | 0.448 | |
| 1b6p | PI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1bdr | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1d4s | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2cej | 1AH | Pol protein | / | 0.447 | |
| 2r5p | MK1 | Gag-Pol polyprotein | / | 0.447 | |
| 3ekq | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3saa | 77F | Protease | / | 0.447 | |
| 1d4k | PI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1eby | BEB | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1t3r | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1hsh | MK1 | Gag-Pol polyprotein | / | 0.445 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3qrs | NK8 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1b6m | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1fff | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1hiv | 1ZK | Gag-Pol polyprotein | / | 0.444 | |
| 1sdv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1yt9 | OIS | Gag-Pol polyprotein | / | 0.444 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3d1z | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3djk | G55 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3lin | E13 | Protease | / | 0.444 | |
| 1hvk | A79 | Gag-Pol polyprotein | / | 0.443 | |
| 1iiq | 0ZR | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2avm | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.443 | |
| 3jvy | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1izh | Q50 | Protease | / | 0.442 | |
| 1mtr | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1mui | AB1 | Protease | / | 0.442 | |
| 1ohr | 1UN | V-1 PROTEASE protein | / | 0.442 | |
| 1zsr | 0ZT | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2qci | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3ckt | YDP | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3el1 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3sa3 | 23X | Protease | / | 0.442 | |
| 1fg6 | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2f3k | RO1 | Protease | / | 0.441 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3qbf | JHG | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4njt | 017 | Protease | / | 0.441 | |
| 1g35 | AHF | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1wbm | BLL | Pol protein | / | 0.440 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.440 | |
| 3kfs | 3TL | Gag-Pol polyprotein | / | 0.440 |