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 |
|---|---|---|---|
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.725 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.631 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.627 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.610 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.597 | |
| 3cse | N22 | Uncharacterized protein | / | 0.592 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.590 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.589 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.589 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.572 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.568 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.565 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.565 | |
| 3qly | 55V | Uncharacterized protein | / | 0.565 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.562 | |
| 3eel | 53T | Uncharacterized protein | / | 0.561 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.559 | |
| 3eek | 53S | Uncharacterized protein | / | 0.558 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.556 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.555 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.550 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.549 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.549 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.547 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.546 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.544 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.542 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.542 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.540 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.536 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.531 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.531 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.530 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 3eej | 53R | Uncharacterized protein | / | 0.529 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.529 | |
| 3eem | 53V | Uncharacterized protein | / | 0.526 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.525 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.525 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.522 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.515 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.514 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.511 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.510 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.509 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.501 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.501 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.497 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.485 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.483 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.479 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.479 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.478 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.469 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.469 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.464 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.460 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3vbq | 0F5 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.459 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.458 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.457 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.456 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1err | RAL | Estrogen receptor | / | 0.455 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.454 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.454 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.454 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3qyo | Q24 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1yhs | STU | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 1rg7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.450 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.447 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.447 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.447 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.446 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.445 | |
| 3bgq | VX2 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.445 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.445 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2rf2 | MRX | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.444 | |
| 3meg | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4c2z | MYA | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.444 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.444 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.442 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3r3b | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.441 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.441 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.441 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.441 | |
| 4ucn | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.440 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 |