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 |
|---|---|---|---|
| 3rix | 923 | Luciferin 4-monooxygenase | 1.13.12.7 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3rix | 923 | Luciferin 4-monooxygenase | 1.13.12.7 | 1.000 | |
| 3ies | M24 | Luciferin 4-monooxygenase | 1.13.12.7 | 0.628 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.488 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.465 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.464 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.461 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.461 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.459 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.459 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.458 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.457 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.457 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.457 | |
| 2ejz | SAH | Diphthine synthase | / | 0.456 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.453 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.453 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.453 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.452 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.452 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.452 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.452 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.451 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.450 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.448 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.448 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 4f4q | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.447 | |
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 | 0.447 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.447 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.446 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.446 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.445 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.444 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.443 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.443 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.443 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.441 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.441 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.441 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.441 | |
| 4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.441 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.440 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2vdg | NDP | Aldose reductase | 1.1.1.21 | 0.440 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.440 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.440 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 |