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 |
|---|---|---|---|
| 4adc | PLP | Succinylornithine transaminase | 2.6.1.81 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4adc | PLP | Succinylornithine transaminase | 2.6.1.81 | 1.000 | |
| 4zwm | PLP | Ornithine aminotransferase, mitochondrial, putative | / | 0.595 | |
| 2oat | PFM | Ornithine aminotransferase, mitochondrial | 2.6.1.13 | 0.571 | |
| 1wkh | PPE | [LysW]-aminoadipate semialdehyde transaminase | / | 0.531 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.489 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.485 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.485 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.481 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.480 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.479 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.476 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.473 | |
| 1wkg | POI | [LysW]-aminoadipate semialdehyde transaminase | / | 0.472 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.469 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.467 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.462 | |
| 2ejz | SAH | Diphthine synthase | / | 0.461 | |
| 3arz | I5I | Chitinase A | / | 0.460 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.458 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.455 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.455 | |
| 1b9i | PXG | 3-amino-5-hydroxybenzoate synthase | 4.2.1.144 | 0.454 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.453 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.452 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.451 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.450 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.449 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2cv1 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.449 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.449 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.448 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 4f3g | KAI | Glutamate receptor 3 | / | 0.448 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.447 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4xcz | T3Q | Qdtf | / | 0.446 | |
| 1vce | SAH | Diphthine synthase | / | 0.445 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.445 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.444 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.443 | |
| 3uk6 | ADP | RuvB-like 2 | 3.6.4.12 | 0.443 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.443 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.442 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.442 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 2e15 | SAH | Diphthine synthase | / | 0.441 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3rba | COD | Phosphopantetheine adenylyltransferase | / | 0.440 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 |