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 |
|---|---|---|---|
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.651 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.639 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.636 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.595 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.588 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.585 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.584 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.582 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.580 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.570 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.567 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.561 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.560 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.555 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.555 | |
| 3eek | 53S | Uncharacterized protein | / | 0.554 | |
| 3eej | 53R | Uncharacterized protein | / | 0.553 | |
| 3cse | N22 | Uncharacterized protein | / | 0.551 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.548 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.544 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.544 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.540 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.540 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.539 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.537 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.537 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.536 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.536 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.535 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.534 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 3eem | 53V | Uncharacterized protein | / | 0.531 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 3eel | 53T | Uncharacterized protein | / | 0.530 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.530 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.528 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.528 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.528 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.527 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.526 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.520 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.514 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.513 | |
| 3qly | 55V | Uncharacterized protein | / | 0.511 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.509 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.506 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.505 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.501 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.500 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.499 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.498 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.497 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.497 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.493 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.493 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.489 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3m09 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.485 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.480 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.472 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.471 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.470 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.470 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.469 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1rx2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.462 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3f8k | COA | Uncharacterized protein | / | 0.461 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3hu3 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.459 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.458 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.456 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.456 | |
| 2eb3 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.454 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.453 | |
| 3lu8 | IQX | Serum albumin | / | 0.453 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.452 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.451 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.448 | |
| 1ysx | 4EB | Serum albumin | / | 0.448 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.448 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.447 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.447 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3ez2 | ADP | Plasmid partition protein A | / | 0.447 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.447 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 1sbr | VIB | Putative HMP/thiamine-binding protein YkoF | / | 0.446 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4v12 | POG | MaoC like domain protein | / | 0.446 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2ynf | WHU | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.445 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1ict | T44 | Transthyretin | / | 0.444 | |
| 1lud | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3qlf | PD5 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.444 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.444 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.444 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.444 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.443 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4l9k | EHF | Serum albumin | / | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vww | 7X2 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.442 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.442 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1qxo | FMN | Chorismate synthase | / | 0.441 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.441 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.441 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.440 |