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 |
|---|---|---|---|
| 3lix | E17 | Protease |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3lix | E17 | Protease | / | 1.000 | |
| 3liq | E14 | Protease | / | 0.580 | |
| 3lin | E13 | Protease | / | 0.544 | |
| 3liv | E16 | Protease | / | 0.516 | |
| 1ec2 | BEJ | Gag-Pol polyprotein | 3.4.23.16 | 0.503 | |
| 2uy0 | HV1 | Gag-Pol polyprotein | 3.4.23.16 | 0.495 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.494 | |
| 2bpz | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.491 | |
| 3lit | E15 | Protease | / | 0.488 | |
| 2bpy | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.484 | |
| 3nu9 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.483 | |
| 1w5v | BE3 | Gag-Pol polyprotein | 3.4.23.16 | 0.482 | |
| 2a4f | AAU | V-1 protease | / | 0.482 | |
| 3s85 | LK0 | Gag-Pol polyprotein | / | 0.482 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.481 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.478 | |
| 2pk5 | 075 | Protease | / | 0.478 | |
| 4hdf | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.478 | |
| 4kb9 | G79 | Protease | / | 0.478 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.477 | |
| 2fxd | DR7 | Pol polyprotein | / | 0.477 | |
| 3i2l | 2NC | Protease | / | 0.477 | |
| 3zps | EQM | Gag-Pol polyprotein | 3.4.23.16 | 0.476 | |
| 3wsj | MK1 | Protease | / | 0.475 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.473 | |
| 1bv7 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 2qd8 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 2qhc | AB1 | Protease | / | 0.472 | |
| 2qnn | QN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 2pk6 | O33 | V-1 protease | / | 0.471 | |
| 2wkz | 5AH | Gag-Pol polyprotein | / | 0.471 | |
| 3a2o | KNJ | Gag-Pol polyprotein | 3.4.23.16 | 0.471 | |
| 3nu6 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.471 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.471 | |
| 1d4s | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 1mes | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 1w5x | BE5 | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 2uxz | HI1 | Gag-Pol polyprotein | 3.4.23.16 | 0.470 | |
| 3ggx | GGX | Gag-Pol polyprotein | / | 0.470 | |
| 1hsh | MK1 | Gag-Pol polyprotein | / | 0.469 | |
| 1wbk | 568 | Pol protein | / | 0.469 | |
| 2ieo | 017 | Protease | / | 0.469 | |
| 2qi5 | MZ7 | Gag-Pol polyprotein | / | 0.469 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 3sa9 | A68 | Protease | / | 0.469 | |
| 1ec0 | BED | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 2bqv | A1A | Protease | / | 0.468 | |
| 2fdd | 385 | Pol protein | / | 0.468 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.468 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 4qgi | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 4ye3 | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 1meu | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 3k4v | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 3s54 | 017 | Protease | / | 0.467 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 1d4l | PI9 | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 1d4y | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 1ivp | 1ZK | Gag-Pol polyprotein | / | 0.466 | |
| 2aqu | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 1c6z | ROC | Protease | / | 0.465 | |
| 1d4k | PI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 1hxw | RIT | Gag-Pol polyprotein | / | 0.465 | |
| 1npa | 3NH | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 1npw | LGZ | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 1sdv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 3ndt | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 1tcx | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 2qak | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 2qd6 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3d1z | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3kdc | JZP | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1g35 | AHF | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 1wbm | BLL | Pol protein | / | 0.463 | |
| 2pqz | G0G | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 3djk | G55 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 3el5 | 1UN | Gag-Pol polyprotein | / | 0.463 | |
| 3sa7 | 55A | Protease | / | 0.463 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 1yt9 | OIS | Gag-Pol polyprotein | / | 0.462 | |
| 2aoe | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 3sa6 | F71 | Protease | / | 0.462 | |
| 1c70 | L75 | Protease | / | 0.461 | |
| 1hiv | 1ZK | Gag-Pol polyprotein | / | 0.461 | |
| 2f3k | RO1 | Protease | / | 0.461 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3ekv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3saa | 77F | Protease | / | 0.461 | |
| 3vfb | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4njv | RIT | Protease | / | 0.461 | |
| 1d4h | BEH | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 1ebz | BEC | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 1hih | C20 | Gag-Pol polyprotein | / | 0.460 | |
| 1hvi | A77 | Protease | / | 0.460 | |
| 1hvj | A78 | Gag-Pol polyprotein | / | 0.460 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 2bpv | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 2f8g | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 3ckt | YDP | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 3kf0 | 3TL | Gag-Pol polyprotein | / | 0.460 | |
| 4a4q | UX9 | Pol protein | / | 0.460 | |
| 4rvj | 478 | Protease | / | 0.460 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1w5y | BE6 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 2b7z | MK1 | Gag-Pol polyprotein | / | 0.459 | |
| 2cej | 1AH | Pol protein | / | 0.459 | |
| 2cem | 2AH | Pol protein | / | 0.459 | |
| 2i4w | KGQ | Protease | / | 0.459 | |
| 2i4x | KGQ | Protease | / | 0.459 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1c6y | MK1 | Protease | / | 0.458 | |
| 1dif | A85 | Gag-Pol polyprotein | / | 0.458 | |
| 1fg6 | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 2hc0 | AB2 | Protease | / | 0.458 | |
| 2hs2 | 017 | Protease | / | 0.458 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 3ttp | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 1d4i | BEG | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2q5k | AB1 | Protease | / | 0.457 | |
| 1ebw | BEI | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1idb | 0DO | Gag-Pol polyprotein | / | 0.456 | |
| 1zsf | 0ZS | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 2xyf | G40 | Gag-Pol polyprotein | / | 0.456 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.456 | |
| 4njs | G08 | Protease | / | 0.456 | |
| 2q64 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3qbf | JHG | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 2i4v | DJR | V-1 protease | / | 0.454 | |
| 3jvy | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 3kfs | 3TL | Gag-Pol polyprotein | / | 0.454 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1fg8 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 1zsr | 0ZT | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2hb3 | GRL | Protease | / | 0.453 | |
| 2nnk | ROC | Protease | / | 0.453 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.453 | |
| 2p3b | 3TL | V-1 protease | / | 0.453 | |
| 2p3d | 3TL | Protease | / | 0.453 | |
| 4djp | M73 | Pol polyprotein | / | 0.453 | |
| 1sdu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2qci | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2qhy | MZ1 | Gag-Pol polyprotein | / | 0.452 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3oxc | ROC | Protease | / | 0.452 | |
| 3qaa | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3qrm | NK7 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 4q1y | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1daz | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1ec1 | BEE | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1qbs | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2cen | 4AH | Protease | / | 0.451 | |
| 2qi0 | MZ3 | Gag-Pol polyprotein | / | 0.451 | |
| 3aid | ARQ | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3mws | 017 | Pol protein | / | 0.451 | |
| 1hvl | A76 | Gag-Pol polyprotein | / | 0.450 | |
| 1sdt | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 2nmy | ROC | Protease | / | 0.450 | |
| 2pyn | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3em6 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3lzv | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 4djr | 0KJ | Pol polyprotein | / | 0.450 | |
| 1eby | BEB | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1ffi | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1sbg | IM1 | Gag-Pol polyprotein | / | 0.449 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3kfn | 3TL | Gag-Pol polyprotein | / | 0.449 | |
| 3mxe | K54 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3ndu | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3ndw | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1qbu | 846 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1t3r | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2i4d | QFI | Protease | / | 0.448 | |
| 2wl0 | 5AH | Gag-Pol polyprotein | / | 0.448 | |
| 2xye | CXG | Gag-Pol polyprotein | / | 0.448 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1b6k | PI5 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1c6x | 3IN | Protease | / | 0.447 | |
| 1g2k | NM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1izh | Q50 | Protease | / | 0.447 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2r3t | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2r5q | 1UN | Gag-Pol polyprotein | / | 0.447 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3ekx | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3ggu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.447 | |
| 3nuj | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3o9d | K19 | Pol polyprotein | / | 0.447 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3qn8 | NI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4dqc | 017 | Gag-Pol polyprotein | / | 0.447 | |
| 1a9m | U0E | Gag-Pol polyprotein | / | 0.446 | |
| 1hii | C20 | Gag-Pol polyprotein | / | 0.446 | |
| 1qbr | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2q54 | MU1 | Protease | / | 0.446 | |
| 3dcr | KVS | Protease | / | 0.446 | |
| 3nu3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3nu4 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4heg | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1ajx | AH1 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1hvk | A79 | Gag-Pol polyprotein | / | 0.445 | |
| 1met | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2a1e | IPF | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2pym | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2qi4 | MZ6 | Gag-Pol polyprotein | / | 0.445 | |
| 2r38 | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2rkf | AB1 | Pol protein | / | 0.445 | |
| 3gi4 | K60 | Gag-Pol polyprotein | / | 0.445 | |
| 3oxw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3sa5 | A69 | Protease | / | 0.445 | |
| 3sac | AF8 | Protease | / | 0.445 | |
| 4djo | MK5 | Pol polyprotein | / | 0.445 | |
| 1hsg | MK1 | Gag-Pol polyprotein | / | 0.444 | |
| 1hxb | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1z1h | HBB | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2qi7 | MZ9 | Gag-Pol polyprotein | / | 0.444 | |
| 3i6o | GR6 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3o9b | K2A | Pol polyprotein | / | 0.444 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1b6p | PI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1hvr | XK2 | Gag-Pol polyprotein | / | 0.443 | |
| 1k1u | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1mtr | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2avm | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2qhz | MZ2 | Gag-Pol polyprotein | / | 0.443 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3nu5 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.443 | |
| 3slz | 3TL | Putative gag-pro-pol polyprotein | / | 0.443 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1bwa | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3cyx | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3o9i | A61 | Gag-Pol polyprotein | / | 0.442 | |
| 3oy4 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3sa3 | 23X | Protease | / | 0.442 | |
| 3uhl | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 4djq | M86 | Pol polyprotein | / | 0.442 | |
| 4dqe | 017 | Gag-Pol polyprotein | / | 0.442 | |
| 4hdb | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 7upj | INU | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1a8g | 2Z4 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1qbt | 146 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1vij | BAY | Gag-Pol polyprotein | / | 0.441 | |
| 2bpx | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3ekp | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3gi6 | D78 | Gag-Pol polyprotein | / | 0.441 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.440 | |
| 3nls | 016 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3o9e | A60 | Pol polyprotein | / | 0.440 | |
| 4nju | TPV | Protease | / | 0.440 |