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 |
|---|---|---|---|
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.637 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.588 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.585 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.534 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.528 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.512 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.510 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.503 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.492 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.491 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.488 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3eek | 53S | Uncharacterized protein | / | 0.486 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.483 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.482 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.480 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.479 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.475 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.474 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.473 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.471 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.467 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.466 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.465 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.465 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.464 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.462 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.461 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1fml | RTL | Retinol dehydratase | / | 0.460 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.459 | |
| 3btj | DEQ | HTH-type transcriptional regulator QacR | / | 0.459 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.458 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.457 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 3eem | 53V | Uncharacterized protein | / | 0.457 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.456 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.456 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 3eej | 53R | Uncharacterized protein | / | 0.455 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.454 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.454 | |
| 2wpx | ACO | Orf14 | / | 0.454 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.454 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.453 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.453 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.452 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.451 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.451 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.450 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.449 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.449 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1dre | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 4xwt | U5P | Ribonuclease J | / | 0.448 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.447 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3qly | 55V | Uncharacterized protein | / | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.447 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.446 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.446 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.446 | |
| 1cde | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.445 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.444 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.443 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.443 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4ho5 | DAU | Glucose-1-phosphate thymidylyltransferase | / | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.442 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.441 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.440 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.440 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.440 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.440 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.440 |