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 |
|---|---|---|---|
| 2jfz | 003 | Glutamate racemase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2jfz | 003 | Glutamate racemase | / | 1.000 | |
| 4b1f | KRH | Glutamate racemase | / | 0.631 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.501 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.496 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.480 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.478 | |
| 4b8w | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.477 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.472 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.471 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.467 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.467 | |
| 4eil | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.466 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.466 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.465 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.465 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.465 | |
| 4iq7 | 1G9 | Mycocyclosin synthase | 1.14.21.9 | 0.464 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.462 | |
| 3vew | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.462 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.461 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.461 | |
| 2wpx | ACO | Orf14 | / | 0.461 | |
| 3vet | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.461 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.460 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3up0 | D7S | aceDAF-12 | / | 0.460 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.460 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.458 | |
| 1zdw | FLV | Prenyltransferase | / | 0.458 | |
| 2c3i | IYZ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.458 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.458 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 3vf2 | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.458 | |
| 4l9q | 9TP | Serum albumin | / | 0.458 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4l8u | 9AZ | Serum albumin | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.456 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.456 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.456 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.456 | |
| 1ddu | DDU | Thymidylate synthase | / | 0.455 | |
| 1osv | CHC | Bile acid receptor | / | 0.455 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.455 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.455 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 1ci7 | CB3 | Thymidylate synthase | 2.1.1.45 | 0.454 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.454 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.454 | |
| 4az0 | S61 | Lysosomal protective protein | 3.4.16.5 | 0.454 | |
| 1e94 | ANP | ATP-dependent protease ATPase subunit HslU | / | 0.453 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.453 | |
| 2hek | GDP | Uncharacterized protein | / | 0.453 | |
| 3a60 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.453 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.453 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.453 | |
| 5cdg | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.452 | |
| 1bq1 | CB3 | Thymidylate synthase | / | 0.451 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.451 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.451 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.451 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.451 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.450 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 3pg3 | DG7 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.450 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4o7u | THF | Thymidylate synthase | / | 0.450 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.450 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.450 | |
| 5cds | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.449 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.449 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.448 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.448 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.448 | |
| 3gdv | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.448 | |
| 3q9z | TXQ | Casein kinase II subunit alpha | 2.7.11.1 | 0.448 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.448 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.447 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.447 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.447 | |
| 3ma3 | 01I | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.446 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.446 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.446 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.446 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.446 | |
| 4iqq | D16 | Thymidylate synthase | / | 0.446 | |
| 1uof | PNN | Deacetoxycephalosporin C synthase | 1.14.20.1 | 0.445 | |
| 3fko | FKO | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3up3 | XCA | aceDAF-12 | / | 0.445 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.445 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.445 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1syn | F89 | Thymidylate synthase | / | 0.444 | |
| 2ay8 | 4TB | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.444 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 2gd2 | CAA | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.444 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4lb2 | DM5 | Serum albumin | / | 0.444 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.444 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.443 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.443 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.443 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.443 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.443 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1g6c | IFP | Thiamine-phosphate synthase | / | 0.442 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.442 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3r32 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.442 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.442 | |
| 3zs5 | SB2 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1juj | LYA | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2hz4 | 4ST | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.441 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2wpw | ACO | Orf14 | / | 0.441 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.441 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.441 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4lm5 | Q17 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.440 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.440 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.440 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.440 | |
| 3zv5 | BPY | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.440 | |
| 4awi | AQ2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.440 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.440 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4i2q | 1BT | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.440 | |
| 5ikq | JMS | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 |