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 |
|---|---|---|---|
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.676 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.631 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.617 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.590 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.586 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.577 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.569 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.565 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.562 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.557 | |
| 3cse | N22 | Uncharacterized protein | / | 0.555 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.555 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.550 | |
| 3eek | 53S | Uncharacterized protein | / | 0.546 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.543 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.540 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.538 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.537 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.536 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.535 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.534 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.532 | |
| 3eej | 53R | Uncharacterized protein | / | 0.531 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.527 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.525 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.524 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.522 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.521 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.521 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.520 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3eem | 53V | Uncharacterized protein | / | 0.517 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.515 | |
| 3eel | 53T | Uncharacterized protein | / | 0.514 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.510 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.508 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.508 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.507 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.506 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.503 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.501 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.494 | |
| 3qly | 55V | Uncharacterized protein | / | 0.494 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.490 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.487 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.486 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.483 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.483 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.476 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.475 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.474 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.472 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.470 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 3m09 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.463 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.460 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.460 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.458 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.456 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.454 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 1rx2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.453 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.452 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2acw | UPG | Glycosyltransferase | / | 0.451 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3gco | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.451 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.450 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.450 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.447 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1sbr | VIB | Putative HMP/thiamine-binding protein YkoF | / | 0.446 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.446 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3f8k | COA | Uncharacterized protein | / | 0.445 | |
| 3pm0 | BHF | Cytochrome P450 1B1 | / | 0.445 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.445 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.441 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.441 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.440 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.440 |