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 |
|---|---|---|---|
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.618 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.618 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.591 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.527 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.515 | |
| 3cse | N22 | Uncharacterized protein | / | 0.512 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.511 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.509 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.507 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.503 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.502 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.501 | |
| 3eek | 53S | Uncharacterized protein | / | 0.498 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.498 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1dre | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.493 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.491 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.490 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.488 | |
| 3eem | 53V | Uncharacterized protein | / | 0.487 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.485 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.484 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.482 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.481 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.480 | |
| 1rh3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3eej | 53R | Uncharacterized protein | / | 0.474 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.470 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.470 | |
| 1fml | RTL | Retinol dehydratase | / | 0.469 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.468 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.464 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.464 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.462 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.462 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 2o12 | FMN | Chorismate synthase | / | 0.458 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.458 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.458 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.458 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.457 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.457 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.455 | |
| 3au8 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.455 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.455 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.454 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.454 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.453 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3qly | 55V | Uncharacterized protein | / | 0.451 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.450 | |
| 1rx2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.449 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1z45 | UPG | Bifunctional protein GAL10 | 5.1.3.2 | 0.448 | |
| 2nn7 | M29 | Carbonic anhydrase 1 | 4.2.1.1 | 0.448 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.448 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4k38 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.448 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.448 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.447 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.447 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.446 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.446 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.445 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.445 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.444 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.444 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.440 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.440 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |