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 |
|---|---|---|---|
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 1.000 | |
| 3rba | COD | Phosphopantetheine adenylyltransferase | / | 0.533 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.510 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.488 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.479 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.471 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.471 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.467 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.464 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.462 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.462 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.462 | |
| 4nau | AGS | Phosphopantetheine adenylyltransferase | / | 0.461 | |
| 3ag6 | PAJ | Pantothenate synthetase | / | 0.460 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.459 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.459 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.459 | |
| 5hg0 | SAM | Pantothenate synthetase | / | 0.459 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.458 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.457 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.456 | |
| 2x3f | APC | Pantothenate synthetase | / | 0.456 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.456 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.455 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.455 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.454 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.454 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.453 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.452 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.452 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.452 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.451 | |
| 4ikz | AFS | Di-tripeptide ABC transporter (Permease) | / | 0.451 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.450 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.450 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.449 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.449 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.449 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.448 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.448 | |
| 3abx | RCB | Glucanase | / | 0.448 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.448 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.447 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.447 | |
| 4e2y | JHZ | Methyltransferase | / | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.446 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.446 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.446 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.445 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.445 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.445 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.444 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.444 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.443 | |
| 1pag | FMP | Antiviral protein I | 3.2.2.22 | 0.443 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.443 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.443 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.443 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.443 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.443 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.442 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3viu | ADP | Phosphoribosylformylglycinamidine synthase subunit PurL | / | 0.442 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.442 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.442 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.441 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.441 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.440 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.440 |