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 |
|---|---|---|---|
| 3keq | NAD | Redox-sensing transcriptional repressor Rex |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3keq | NAD | Redox-sensing transcriptional repressor Rex | / | 1.000 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.486 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.478 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.478 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.477 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.477 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.473 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.473 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.473 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.472 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.471 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.470 | |
| 2bxo | OPB | Serum albumin | / | 0.468 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.467 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.466 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.466 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.462 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.462 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.462 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.461 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.460 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.460 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.460 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.460 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.458 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.458 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.457 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.457 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.457 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.455 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.454 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.453 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.453 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.453 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.453 | |
| 1tys | TMP | Thymidylate synthase | / | 0.452 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.452 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.452 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.452 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.452 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.450 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.450 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4oe4 | NAD | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | 1.2.1.88 | 0.450 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.449 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.449 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.449 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.449 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.449 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.448 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.448 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.448 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.447 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.446 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.446 | |
| 4eqr | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.446 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.445 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
| 3r43 | ID8 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.444 | |
| 3reo | EUG | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.444 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.444 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.444 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.443 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.443 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.443 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.443 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.443 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.442 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.442 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.442 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.442 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 1fml | RTL | Retinol dehydratase | / | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.441 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.441 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.441 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.441 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |