sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4ld2 | CTN | Cytidine and deoxycytidylate deaminase zinc-binding region |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ld2 | CTN | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 1.000 | |
| 4hrq | AZG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.574 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.481 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.477 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.473 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.472 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.472 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.461 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.458 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.457 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.456 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.455 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.453 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.452 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.451 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.448 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.447 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.447 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.446 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.445 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.445 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.445 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.444 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.443 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.443 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.441 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.440 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 |