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 |
|---|---|---|---|
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 1.000 | |
| 3eek | 53S | Uncharacterized protein | / | 0.637 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.611 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.608 | |
| 3qly | 55V | Uncharacterized protein | / | 0.606 | |
| 3cse | N22 | Uncharacterized protein | / | 0.600 | |
| 3eej | 53R | Uncharacterized protein | / | 0.595 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.592 | |
| 3eel | 53T | Uncharacterized protein | / | 0.590 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.586 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.579 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.577 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.575 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.575 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.574 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.571 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.570 | |
| 3eem | 53V | Uncharacterized protein | / | 0.568 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.567 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.564 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.563 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.562 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.561 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.560 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.556 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.556 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.555 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.551 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.551 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.551 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.543 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.536 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.534 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.533 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.532 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.531 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.531 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.528 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.527 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.527 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.524 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.517 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.515 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.515 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.515 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.514 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.514 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.511 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.511 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.511 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.508 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.507 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.503 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.502 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.502 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.502 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.496 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.492 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.489 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.487 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.486 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.483 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.483 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.482 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.482 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.481 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.480 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.478 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.467 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3k45 | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.464 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.463 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.461 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4xwt | U5P | Ribonuclease J | / | 0.461 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.460 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.460 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.459 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.459 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1ek2 | CDU | Bifunctional epoxide hydrolase 2 | / | 0.456 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.456 | |
| 1fml | RTL | Retinol dehydratase | / | 0.455 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.455 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.453 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.452 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.451 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.451 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.451 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.448 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.448 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.445 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4m7v | RAR | Dihydrofolate reductase | / | 0.445 | |
| 2jed | LG8 | Protein kinase C theta type | 2.7.11.13 | 0.444 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.444 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.444 | |
| 3ezp | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.442 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.441 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.441 | |
| 3lu8 | IQX | Serum albumin | / | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4iv2 | 1GR | Estrogen receptor | / | 0.441 | |
| 1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.440 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.440 |