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 |
|---|---|---|---|
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 1.000 | |
| 4ax8 | ADP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.529 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.481 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.481 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.478 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.475 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.469 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.468 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.464 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.464 | |
| 5cvh | ADP | Casein kinase II subunit alpha | 2.7.11.1 | 0.463 | |
| 2rab | NAD | Glutathione amide reductase | / | 0.460 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.459 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.458 | |
| 4ock | ANP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.458 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.457 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.456 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.455 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.455 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.455 | |
| 4fi1 | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.454 | |
| 1r2j | FAD | FkbI | / | 0.453 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.453 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.452 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.451 | |
| 2w6m | OA1 | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 4mq2 | 2C4 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.447 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 2xj2 | 985 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.445 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.445 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.445 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.444 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.444 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.443 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.443 | |
| 4lfi | GNP | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.442 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.441 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 4py6 | R78 | Bromodomain protein, putative | / | 0.441 | |
| 3zxz | KRW | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 4qmy | STU | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.440 |