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 |
|---|---|---|---|
| 4n1g | CEI | Obelin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4n1g | CEI | Obelin | / | 1.000 | |
| 4iae | 1DX | Alr2278 protein | / | 0.485 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.472 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.472 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.471 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.470 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.469 | |
| 4i52 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.466 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.464 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.462 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.461 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.460 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.459 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.457 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.457 | |
| 1s36 | CEI | Obelin | / | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.456 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.456 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.454 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 4iah | 1DX | Alr2278 protein | / | 0.454 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.453 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.453 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.452 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.452 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4nqg | CZH | Mitrocomin | / | 0.452 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.451 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.451 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.448 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 1uhh | CZP | Aequorin-2 | / | 0.447 | |
| 1eio | GCH | Gastrotropin | / | 0.446 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.446 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.446 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.446 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.445 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.445 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.445 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.445 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.444 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.444 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.442 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.441 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.441 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.441 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 |