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 |
|---|---|---|---|
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.701 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.641 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.637 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.635 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.631 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.629 | |
| 3qly | 55V | Uncharacterized protein | / | 0.628 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.621 | |
| 3eel | 53T | Uncharacterized protein | / | 0.610 | |
| 3cse | N22 | Uncharacterized protein | / | 0.603 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.598 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.596 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.591 | |
| 3eek | 53S | Uncharacterized protein | / | 0.588 | |
| 3eem | 53V | Uncharacterized protein | / | 0.580 | |
| 3eej | 53R | Uncharacterized protein | / | 0.578 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.572 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.571 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.568 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.565 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.565 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.563 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.562 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.553 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.549 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.549 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.548 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.545 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.539 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.539 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.535 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.535 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.533 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.531 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.530 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.526 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.517 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.511 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.499 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.499 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.493 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.492 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.490 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.488 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.488 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.485 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.483 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.483 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.481 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 2vqo | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.479 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.479 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.477 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.474 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.470 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.469 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.469 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.469 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.466 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.465 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.462 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.459 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.459 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3ue4 | DB8 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.456 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.456 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 3dmj | GWE | Pol protein | / | 0.455 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.455 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.454 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4iv2 | 1GR | Estrogen receptor | / | 0.454 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.453 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.453 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.452 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.451 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.450 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4m7v | RAR | Dihydrofolate reductase | / | 0.450 | |
| 3tub | FPU | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.449 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3a0i | AJI | Glucokinase | 2.7.1.2 | 0.448 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.448 | |
| 4m6k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.447 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.446 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3k45 | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4b8m | VX6 | Aurora kinase B-A | 2.7.11.1 | 0.446 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.445 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.445 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.445 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.445 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.445 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.445 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.444 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 4iw8 | KN3 | Estrogen receptor | / | 0.444 | |
| 4qa1 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 5bsr | COA | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.444 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.443 | |
| 1rg7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.443 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.443 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.443 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.442 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.442 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.442 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.440 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.440 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.440 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.440 |