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 |
|---|---|---|---|
| 2uz1 | TPP | Benzaldehyde lyase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2uz1 | TPP | Benzaldehyde lyase | / | 1.000 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.587 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.536 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.525 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.489 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.478 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2q5o | PPY | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.473 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.471 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.471 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.470 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.470 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.468 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.463 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.462 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.462 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.461 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.460 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.459 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.456 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.456 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.456 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.455 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.455 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.453 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.453 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.452 | |
| 2ejz | SAH | Diphthine synthase | / | 0.451 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 3otq | MZL | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.449 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.448 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.448 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.448 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 1fml | RTL | Retinol dehydratase | / | 0.447 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.447 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.445 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.445 | |
| 2ji6 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.444 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.444 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.443 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.443 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.443 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.443 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.442 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.441 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.440 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.440 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.440 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2y3r | TIR | TamL | / | 0.440 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.440 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |