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 |
|---|---|---|---|
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.579 | |
| 3cse | N22 | Uncharacterized protein | / | 0.563 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.547 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.545 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.542 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.542 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.539 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.536 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.535 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.535 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.533 | |
| 3eek | 53S | Uncharacterized protein | / | 0.531 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.531 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.530 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.526 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.523 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.513 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.513 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.512 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 3eej | 53R | Uncharacterized protein | / | 0.508 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.507 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.505 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.502 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.500 | |
| 3eel | 53T | Uncharacterized protein | / | 0.499 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.495 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.494 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.493 | |
| 3eem | 53V | Uncharacterized protein | / | 0.493 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.486 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.482 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.480 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.480 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.479 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.479 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.479 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.477 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.476 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.476 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.476 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.475 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.475 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.474 | |
| 3qly | 55V | Uncharacterized protein | / | 0.473 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.472 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.472 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.469 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.468 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.467 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.467 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.467 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.465 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.465 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.465 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.462 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.462 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.461 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.459 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.458 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.457 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1tlc | F89 | Thymidylate synthase | / | 0.456 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4l8u | 9AZ | Serum albumin | / | 0.455 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.455 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.454 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 4v12 | POG | MaoC like domain protein | / | 0.454 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.454 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.453 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3iqz | H4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.452 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.452 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.452 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.451 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.451 | |
| 3zuy | TCH | Transporter | / | 0.451 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.451 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.450 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.450 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.448 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.446 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.446 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.446 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 1sej | F89 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.444 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.444 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.444 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.444 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.444 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.444 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2bxm | IMN | Serum albumin | / | 0.443 | |
| 2y4g | TIR | TamL | / | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.443 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.443 | |
| 3u9e | COA | Lmo1369 protein | / | 0.443 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.443 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.443 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3iqf | E4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.442 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 4ezj | 0SC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.442 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.441 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.441 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.441 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.440 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.440 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.440 | |
| 3gob | HXX | DdmC | / | 0.440 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.440 |