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 |
|---|---|---|---|
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.751 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.679 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.664 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.645 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.644 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.644 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.636 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.635 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.620 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.620 | |
| 4qjc | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.612 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.607 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.599 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.599 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.593 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.587 | |
| 1dlr | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.574 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.546 | |
| 3cse | N22 | Uncharacterized protein | / | 0.545 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.544 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.537 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.533 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.526 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.523 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.522 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 3eek | 53S | Uncharacterized protein | / | 0.522 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.522 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.521 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.518 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.517 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.514 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.510 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.507 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.507 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.504 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.487 | |
| 3eej | 53R | Uncharacterized protein | / | 0.486 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.485 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3eel | 53T | Uncharacterized protein | / | 0.484 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.481 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.478 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.475 | |
| 3eem | 53V | Uncharacterized protein | / | 0.474 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.471 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.470 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.469 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4m6k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.458 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.457 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.457 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.451 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.450 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.450 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.450 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.449 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.445 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.443 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1fml | RTL | Retinol dehydratase | / | 0.441 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.441 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.440 |