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 |
|---|---|---|---|
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 1.000 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.812 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.787 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.781 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.698 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.566 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.538 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.487 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.486 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.486 | |
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.477 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.477 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.475 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.471 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.471 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.471 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.471 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.471 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.470 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.468 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.466 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.466 | |
| 1n95 | FTH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.464 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.463 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.458 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.458 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.457 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.457 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.455 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.455 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.455 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.455 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.453 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.453 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.453 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.453 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.452 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.452 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.452 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.451 | |
| 2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.450 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.450 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.450 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.449 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.449 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.449 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.448 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.448 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.447 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.447 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1e2n | RCA | Thymidine kinase | / | 0.446 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2cv1 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.446 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.446 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.445 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.444 | |
| 4kxj | P34 | Nucleoprotein | / | 0.444 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.444 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.443 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.443 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.443 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.443 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.443 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.443 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.442 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.442 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.442 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.442 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.441 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.441 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.441 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.440 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.440 |