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 |
|---|---|---|---|
| 2hv7 | ADP | Serine/threonine-protein phosphatase 2A activator | 5.2.1.8 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2hv7 | ADP | Serine/threonine-protein phosphatase 2A activator | 5.2.1.8 | 1.000 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.478 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.478 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.478 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.478 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.478 | |
| 3csc | ACO | Citrate synthase, mitochondrial | 2.3.3.1 | 0.466 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.466 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.461 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.460 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.457 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.457 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.457 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.456 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.455 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.454 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.454 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.454 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.452 | |
| 3ts1 | TYA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.452 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.452 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.451 | |
| 4iva | 1J5 | Tyrosine-protein kinase JAK2 | / | 0.450 | |
| 4kwh | NAP | Reductase homolog | / | 0.450 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.449 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.449 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.448 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.448 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.448 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.448 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.448 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.447 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.447 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.447 | |
| 1csc | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.446 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.446 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.446 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.446 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 2cts | COA | Citrate synthase, mitochondrial | 2.3.3.1 | 0.445 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3clx | X22 | E3 ubiquitin-protein ligase XIAP | 6.3.2 | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.445 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.444 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 3uib | SB2 | Putative mitogen-activated protein kinase | / | 0.444 | |
| 5a3c | NAD | SIR2 family protein | / | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.443 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.443 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.442 | |
| 2h12 | CMX | Citrate synthase | / | 0.442 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.442 | |
| 5cts | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.442 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.441 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.441 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 |