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 |
|---|---|---|---|
| 3jwc | EKB | Dihydrofolate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3jwc | EKB | Dihydrofolate reductase | / | 1.000 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.600 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.566 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 3eek | 53S | Uncharacterized protein | / | 0.553 | |
| 3cse | N22 | Uncharacterized protein | / | 0.545 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.545 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.545 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.544 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.539 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.536 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.534 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.532 | |
| 3eel | 53T | Uncharacterized protein | / | 0.529 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.528 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.527 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.526 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 3qly | 55V | Uncharacterized protein | / | 0.516 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.514 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 3eem | 53V | Uncharacterized protein | / | 0.512 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.511 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.510 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.509 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.509 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.508 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.503 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.499 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.499 | |
| 3eej | 53R | Uncharacterized protein | / | 0.498 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.497 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.496 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.495 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.493 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.493 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.492 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.489 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.486 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.484 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.481 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.479 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.478 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.475 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.474 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.473 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.469 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.463 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.461 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.460 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.459 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.457 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.456 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.455 | |
| 3aba | FLI | Cytochrome P450 | / | 0.453 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3q30 | D61 | Squalene synthase | 2.5.1.21 | 0.453 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3och | 2MX | 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 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.450 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.450 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.450 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.449 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.449 | |
| 3qyo | Q24 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.448 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.448 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.448 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 1jut | LYD | Thymidylate synthase | / | 0.447 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1zhz | ERG | Oxysterol-binding protein homolog 4 | / | 0.447 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.447 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.447 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.445 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.444 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.444 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.444 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.444 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.443 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.441 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.441 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.440 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.440 |