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 |
|---|---|---|---|
| 2c3y | HTL | Pyruvate synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2c3y | HTL | Pyruvate synthase | / | 1.000 | |
| 1kek | HTL | Pyruvate synthase | / | 0.641 | |
| 2uza | HTL | Pyruvate synthase | / | 0.602 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.594 | |
| 2pda | TPP | Pyruvate synthase | / | 0.570 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.567 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.566 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.527 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.527 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.524 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.496 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.484 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.482 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.471 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.468 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.468 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.467 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.467 | |
| 1e0a | GNP | Cell division control protein 42 homolog | / | 0.466 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.465 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.458 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.457 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.456 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.456 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.455 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.455 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.454 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.454 | |
| 4irn | FAD | AnaB | / | 0.454 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 1lhw | ESM | Sex hormone-binding globulin | / | 0.452 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.451 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 4feu | 537 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.451 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.451 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.451 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.450 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.450 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.449 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.449 | |
| 1qxo | FMN | Chorismate synthase | / | 0.449 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.449 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.447 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.447 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.446 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.446 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.446 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4edf | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.446 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.445 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.445 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.444 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.443 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.443 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.443 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.443 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.443 | |
| 4zth | GG5 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3btj | DEQ | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3elm | 24F | Collagenase 3 | 3.4.24 | 0.441 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.441 | |
| 3zcb | ATP | Adenosine monophosphate-protein transferase VbhT | 2.7.7.n1 | 0.441 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1axw | MTX | Thymidylate synthase | / | 0.440 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.440 | |
| 2yis | I46 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.440 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.440 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.440 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.440 |