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 |
|---|---|---|---|
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.697 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.656 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.647 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.634 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.624 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.613 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.593 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.588 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.580 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.580 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.559 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.550 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.544 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.541 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.540 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.540 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.536 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.536 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.534 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 3qly | 55V | Uncharacterized protein | / | 0.515 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.513 | |
| 3eek | 53S | Uncharacterized protein | / | 0.512 | |
| 3eel | 53T | Uncharacterized protein | / | 0.510 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.510 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.507 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.503 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.500 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.500 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.497 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.491 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.490 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.489 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 3cse | N22 | Uncharacterized protein | / | 0.488 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.487 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.487 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.484 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.482 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.481 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.480 | |
| 3eej | 53R | Uncharacterized protein | / | 0.480 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.479 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.472 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.471 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.469 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.467 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.467 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4ug7 | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.467 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.464 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.463 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.462 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4ug7 | 1EV | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.461 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.461 | |
| 3eem | 53V | Uncharacterized protein | / | 0.460 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.460 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.459 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.459 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.458 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.458 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.458 | |
| 4lux | QJ8 | Nitric oxide synthase, brain | 1.14.13.39 | 0.458 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.458 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.457 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.455 | |
| 3dmj | GWE | Pol protein | / | 0.455 | |
| 3nlj | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.455 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.454 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.454 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.454 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.453 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.453 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.452 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.451 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.451 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3aba | FLI | Cytochrome P450 | / | 0.449 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.449 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3qyo | Q24 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.449 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3rqm | X2E | Nitric oxide synthase, brain | 1.14.13.39 | 0.448 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.448 | |
| 4cx3 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.448 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.446 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.446 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.445 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.445 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.444 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3zhb | NAP | Putative dehydrogenase | / | 0.444 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.443 | |
| 4boe | CLR | Japanin | / | 0.443 | |
| 4cx3 | HW8 | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 4eux | HW1 | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.443 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.442 | |
| 3nlj | JRR | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.441 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.441 | |
| 4imw | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.440 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.440 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3i0r | RT3 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3lan | KBT | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3svp | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 4gkh | 0J9 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.440 |