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 |
|---|---|---|---|
| 2avx | HTF | Regulatory protein SdiA |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2avx | HTF | Regulatory protein SdiA | / | 1.000 | |
| 4y17 | LAE | Transcriptional regulator of ftsQAZ gene cluster | / | 0.537 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.509 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.502 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.486 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.480 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.477 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.474 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.473 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.469 | |
| 3qp8 | HL0 | Transcriptional activator, LuxR/UhpA family of regulators | / | 0.468 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.466 | |
| 1c7o | PPG | Hemolysin | / | 0.465 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.463 | |
| 1vf2 | GTX | Glutathione S-transferase 3 | 2.5.1.18 | 0.462 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.462 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.461 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.461 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.460 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.460 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.460 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.460 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.459 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1dqa | COA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.456 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.455 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.454 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.452 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.452 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.451 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.450 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.449 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.449 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.449 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.448 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.448 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 2nr4 | FMN | Conserved protein | / | 0.446 | |
| 3tvq | DQH | Multifunctional cyclase-dehydratase-3-O-methyl transferase TcmN | 2.1.1 | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4iah | 1DX | Alr2278 protein | / | 0.446 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.445 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.445 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.445 | |
| 4blc | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.445 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 3b9l | AZZ | Serum albumin | / | 0.444 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.443 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.442 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.441 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.441 | |
| 1xp8 | AGS | Protein RecA | / | 0.440 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.440 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.440 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 4iae | 1DX | Alr2278 protein | / | 0.440 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.440 |