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 |
|---|---|---|---|
| 2g00 | 4QC | Coagulation factor X | 3.4.21.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2g00 | 4QC | Coagulation factor X | 3.4.21.6 | 1.000 | |
| 4btu | 6XS | Coagulation factor X | 3.4.21.6 | 0.559 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.525 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.515 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.512 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.499 | |
| 3v0x | ANH | Cationic trypsin | 3.4.21.4 | 0.494 | |
| 1iqe | XMB | Coagulation factor X | 3.4.21.6 | 0.492 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.492 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.490 | |
| 4bti | 7R9 | Coagulation factor X | 3.4.21.6 | 0.490 | |
| 2cji | GSK | Coagulation factor X | 3.4.21.6 | 0.488 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.481 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.480 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.479 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.479 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.477 | |
| 1vja | 7IN | Urokinase-type plasminogen activator | 3.4.21.73 | 0.476 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.474 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.473 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.473 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.473 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.472 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.472 | |
| 1nfy | RTR | Coagulation factor X | 3.4.21.6 | 0.471 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.470 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.469 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.468 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.467 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.467 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.466 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.464 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.463 | |
| 1iqg | XME | Coagulation factor X | 3.4.21.6 | 0.462 | |
| 2iml | FMN | Uncharacterized protein | / | 0.461 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.461 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.458 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.458 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.456 | |
| 1hon | GNH | Adenylosuccinate synthetase | / | 0.454 | |
| 3wag | TYD | Glycosyltransferase | / | 0.454 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.451 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.450 | |
| 2y5h | Y5H | Coagulation factor X | 3.4.21.6 | 0.450 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 3plp | BBA | Cationic trypsin | 3.4.21.4 | 0.450 | |
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.449 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.447 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.447 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.447 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.447 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.447 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.446 | |
| 4nvk | 2NY | Peroxidase | / | 0.446 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.445 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.445 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.445 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.445 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.444 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.444 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 2udp | UPP | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.443 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.442 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.442 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.441 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.441 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.440 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.440 |