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 |
|---|---|---|---|
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.694 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.657 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.631 | |
| 3cse | N22 | Uncharacterized protein | / | 0.629 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.619 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.618 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.616 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.612 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.607 | |
| 3qly | 55V | Uncharacterized protein | / | 0.606 | |
| 3eej | 53R | Uncharacterized protein | / | 0.604 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.604 | |
| 3eem | 53V | Uncharacterized protein | / | 0.598 | |
| 3eel | 53T | Uncharacterized protein | / | 0.597 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.594 | |
| 3eek | 53S | Uncharacterized protein | / | 0.593 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.589 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.580 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.575 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.574 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.568 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.566 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.565 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.562 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.562 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.555 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.555 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.555 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.555 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.551 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.551 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.549 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.546 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.546 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.541 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.540 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.535 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.534 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.529 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.528 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.527 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.526 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.523 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.521 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.519 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.517 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.516 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.514 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.510 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.509 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.508 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.506 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.503 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.503 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.502 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.499 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.499 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.498 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.495 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.494 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.494 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.494 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.494 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.492 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.492 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.491 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.490 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.488 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.487 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.486 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.484 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.477 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.474 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.474 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.465 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.464 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.462 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.461 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1err | RAL | Estrogen receptor | / | 0.459 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.459 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.458 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.458 | |
| 1rg7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 4iv2 | 1GR | Estrogen receptor | / | 0.455 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.453 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.452 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.451 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.449 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.448 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.447 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.447 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.447 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.446 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.446 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.446 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.445 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.445 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.445 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.444 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.443 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.443 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.442 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3q5k | D1U | Heat shock protein 83-1 | / | 0.442 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.441 | |
| 3cx5 | SMA | Cytochrome b | / | 0.441 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 2bxm | IMN | Serum albumin | / | 0.440 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.440 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.440 |