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 |
|---|---|---|---|
| 3mtw | M3R | Xaa-Pro dipeptidase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3mtw | M3R | Xaa-Pro dipeptidase, putative | / | 1.000 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.509 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.494 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.489 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.468 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.465 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.465 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.458 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.457 | |
| 4eqw | COA | Coenzyme A disulfide reductase | / | 0.456 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.455 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.454 | |
| 1w29 | TS0 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4e2y | JHZ | Methyltransferase | / | 0.453 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.450 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.450 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.449 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.449 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.449 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.448 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.448 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.448 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1tys | DHF | Thymidylate synthase | / | 0.446 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.446 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 4xmx | BES | Aminopeptidase N | 3.4.11.2 | 0.445 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.444 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.444 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.442 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 3e6y | CW1 | 14-3-3-like protein C | / | 0.441 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.440 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 |