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 |
|---|---|---|---|
| 2y42 | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2y42 | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 1.000 | |
| 3kxw | 1ZZ | Saframycin Mx1 synthetase B | / | 0.499 | |
| 3fwy | ADP | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein | / | 0.490 | |
| 3e8x | NAP | BH1520 protein | / | 0.489 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.487 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.477 | |
| 4hn1 | TYD | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.475 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.472 | |
| 3lnv | 1ZZ | Saframycin Mx1 synthetase B | / | 0.471 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.468 | |
| 1f52 | ADP | Glutamine synthetase | 6.3.1.2 | 0.467 | |
| 1esq | TZP | Hydroxyethylthiazole kinase | / | 0.466 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.465 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.464 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.464 | |
| 2rir | NAP | Dipicolinate synthase subunit A | / | 0.463 | |
| 4ffm | ADP | Uncharacterized protein | / | 0.463 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.462 | |
| 2xcl | ANP | Phosphoribosylamine--glycine ligase | / | 0.462 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.462 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.462 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.461 | |
| 2g89 | UMP | Thymidylate synthase | / | 0.460 | |
| 4k81 | GTP | GTPase HRas | / | 0.460 | |
| 4yqf | GDP | Septin-9 | / | 0.460 | |
| 5kje | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.459 | |
| 5cdg | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.459 | |
| 3sop | GDP | Neuronal-specific septin-3 | / | 0.458 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.458 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.458 | |
| 2pz8 | APC | NH(3)-dependent NAD(+) synthetase | / | 0.457 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.457 | |
| 3mpi | GRA | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.457 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.457 | |
| 4h50 | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.457 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.456 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.455 | |
| 5aga | ANP | DNA polymerase theta | / | 0.455 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.454 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.454 | |
| 4je7 | BB2 | Peptide deformylase 1A, chloroplastic/mitochondrial | 3.5.1.88 | 0.454 | |
| 2rc3 | NAD | CBS domain | / | 0.453 | |
| 3ftq | GNP | Septin-2 | / | 0.453 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.453 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.452 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.452 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.452 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.452 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 3lm8 | VIB | Thiamine pyrophosphokinase | 2.7.6.2 | 0.451 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.450 | |
| 4oaq | NDP | R-specific carbonyl reductase | / | 0.450 | |
| 3gyq | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.449 | |
| 3rba | COD | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 4ohx | ADP | Protein clpf-1 | / | 0.449 | |
| 3amt | ATP | tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS | 6.3.4.22 | 0.448 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.447 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.447 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 2wvj | TTP | Thymidine kinase, cytosolic | 2.7.1.21 | 0.447 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.447 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.447 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.447 | |
| 4hs4 | FMN | Chromate reductase | / | 0.447 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1a71 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 3td7 | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.446 | |
| 5eso | ISC | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.446 | |
| 1fpy | ADP | Glutamine synthetase | 6.3.1.2 | 0.445 | |
| 1il0 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.445 | |
| 4m2a | UPG | UDP-glucose pyrophosphorylase | / | 0.445 | |
| 1b7t | ADP | Myosin heavy chain, striated muscle | / | 0.444 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.444 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.444 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.444 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 3oq6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.444 | |
| 1jvd | UD1 | UDP-N-acetylhexosamine pyrophosphorylase | 2.7.7.23 | 0.443 | |
| 1lj8 | NAD | Mannitol dehydrogenase | / | 0.443 | |
| 3asj | XYM | Homoisocitrate dehydrogenase | / | 0.443 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.443 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.443 | |
| 1axe | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1u80 | C5P | Coenzyme A biosynthesis bifunctional protein CoaBC | 6.3.2.5 | 0.442 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.442 | |
| 2vnj | NAP | NADPH:ferredoxin reductase | / | 0.442 | |
| 3ulk | NDP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.442 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.442 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.442 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1pxj | CK2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.441 | |
| 2r26 | CMC | Citrate synthase | 2.3.3.16 | 0.441 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.441 | |
| 4azm | T4B | Fatty acid-binding protein, epidermal | / | 0.441 | |
| 4f5d | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4z54 | GDP | Neuronal-specific septin-3 | / | 0.441 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.440 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1yp4 | ADQ | Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic | 2.7.7.27 | 0.440 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.440 | |
| 2g8a | UMP | Thymidylate synthase | / | 0.440 | |
| 3hf3 | FMN | Chromate reductase | / | 0.440 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.440 | |
| 3vo8 | GDP | Cell division protein FtsZ | / | 0.440 | |
| 4eiq | KCT | Putative FAD-monooxygenase | / | 0.440 | |
| 4hi0 | GDP | Urease accessory protein UreG | / | 0.440 | |
| 4qxp | 1YE | Stimulator of interferon genes protein | / | 0.440 | |
| 5cds | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |