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 |
|---|---|---|---|
| 3e9s | TTT | Replicase polyprotein 1ab | 3.4.22 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3e9s | TTT | Replicase polyprotein 1ab | 3.4.22 | 1.000 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.497 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.474 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.472 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.470 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.466 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.465 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.463 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.462 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.462 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.462 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.461 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.459 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.457 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.457 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.456 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.456 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.455 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.455 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.455 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.455 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2c97 | JCL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.454 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.453 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.452 | |
| 4rel | KMP | Glycosyltransferase | / | 0.452 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.451 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.451 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.450 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1qs2 | NAD | Vip2Ac | / | 0.449 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.449 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.449 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.449 | |
| 1e2n | RCA | Thymidine kinase | / | 0.448 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.448 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.448 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.448 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1bl4 | AP1 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 1qy2 | IPZ | Major urinary protein 1 | / | 0.447 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.447 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.447 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.447 | |
| 5dn1 | AMZ | Phosphoribosyl isomerase A | 5.3.1.16 | 0.447 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.446 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.445 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.445 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.445 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.444 | |
| 1map | KET | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.444 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 3c0z | SHH | Histone deacetylase 7 | 3.5.1.98 | 0.444 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.443 | |
| 1fki | SB1 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2f6r | ACO | Bifunctional coenzyme A synthase | / | 0.443 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.443 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.443 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.443 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2clm | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.441 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3w0t | HPU | Lactoylglutathione lyase | 4.4.1.5 | 0.441 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1syn | F89 | Thymidylate synthase | / | 0.440 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.440 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 4phl | PIL | Phosphodiesterase | / | 0.440 |