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 |
|---|---|---|---|
| 4gm0 | TZD | Benzoylformate decarboxylase | 4.1.1.7 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4gm0 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.000 | |
| 4jd5 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.767 | |
| 4qel | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.626 | |
| 4mq5 | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.582 | |
| 4ju8 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.555 | |
| 1bfd | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.539 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.519 | |
| 5dgt | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.517 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.505 | |
| 4gm1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.504 | |
| 2fwn | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.500 | |
| 4mzx | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.500 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.494 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.480 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.469 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.469 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.467 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.463 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.462 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.461 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.459 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.457 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.455 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.454 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.452 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.451 | |
| 2wb2 | FAD | RE11660p | / | 0.451 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.450 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.449 | |
| 4h4w | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.449 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.448 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.447 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4ju9 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.446 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.445 | |
| 5c3j | UQ1 | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | / | 0.445 | |
| 5c3j | UQ1 | Succinate dehydrogenase cytochrome b560 | / | 0.445 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.444 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.443 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.442 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.441 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.441 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3csc | ACO | Citrate synthase, mitochondrial | 2.3.3.1 | 0.441 | |
| 3nt6 | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.441 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.440 |