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 |
|---|---|---|---|
| 1ht2 | ADP | ATP-dependent protease ATPase subunit HslU |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1ht2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 1.000 | |
| 1e94 | ANP | ATP-dependent protease ATPase subunit HslU | / | 0.600 | |
| 1im2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.548 | |
| 1g41 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.535 | |
| 4fcw | ADP | Chaperone protein ClpB | / | 0.525 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.507 | |
| 4fd2 | ADP | Chaperone protein ClpB | / | 0.507 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.505 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.502 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.500 | |
| 2phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.492 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.487 | |
| 1ofh | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.487 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.482 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.479 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.475 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.473 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.473 | |
| 2c9c | ATP | Psp operon transcriptional activator | / | 0.469 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.469 | |
| 4cta | ATP | CinA-like protein | / | 0.469 | |
| 5iqe | GNP | Bifunctional AAC/APH | 2.3.1 | 0.469 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.468 | |
| 1gld | ADP | Glycerol kinase | / | 0.467 | |
| 1s3s | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.467 | |
| 4qos | ADP | Psp operon transcriptional activator | / | 0.467 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.466 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.465 | |
| 3dzd | ADP | Transcriptional regulator (NtrC family) | / | 0.465 | |
| 1ny5 | ADP | Transcriptional regulator (NtrC family) | / | 0.464 | |
| 5iqf | GDP | Bifunctional AAC/APH | 2.3.1 | 0.464 | |
| 4jbo | WPH | Aurora kinase A | 2.7.11.1 | 0.462 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.458 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.458 | |
| 3lpb | NVB | Tyrosine-protein kinase JAK2 | / | 0.457 | |
| 4ki8 | ADP | 60 kDa chaperonin | / | 0.457 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.456 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.456 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.455 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.454 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.454 | |
| 4jlo | ADP | Adenylate kinase | / | 0.454 | |
| 1dvr | ATF | Adenylate kinase | / | 0.453 | |
| 3vth | APC | Carbamoyltransferase | / | 0.453 | |
| 4fl2 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.453 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.453 | |
| 4ork | GDP | Bifunctional AAC/APH | 2.3.1 | 0.453 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1hk3 | T44 | Serum albumin | / | 0.452 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.452 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.452 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.451 | |
| 4jky | ADP | Adenylate kinase | / | 0.451 | |
| 4lj8 | ADP | Chaperone protein ClpB | / | 0.451 | |
| 1um8 | ADP | ATP-dependent Clp protease ATP-binding subunit ClpX | / | 0.450 | |
| 3hrf | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.450 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.450 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.450 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.449 | |
| 3nbv | ANP | Ketohexokinase | / | 0.448 | |
| 4mq1 | 2C3 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.448 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 2r4t | ADP | Glycogen synthase | 2.4.1.21 | 0.447 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.447 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 4e07 | ACP | Plasmid partitioning protein ParF | / | 0.447 | |
| 4oa9 | ANP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.447 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 2ycr | HCW | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.446 | |
| 3orz | BI4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 4xj3 | GTP | Cyclic GMP-AMP synthase | / | 0.446 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.445 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.445 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4hse | ADP | Chaperone protein ClpB | / | 0.445 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.444 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.444 | |
| 4hjf | C2E | GGDEF family protein | / | 0.444 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.444 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.444 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.444 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.443 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.443 | |
| 2z7q | ACP | Ribosomal protein S6 kinase alpha-1 | 2.7.11.1 | 0.443 | |
| 3u9e | COA | Lmo1369 protein | / | 0.443 | |
| 4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.443 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.443 | |
| 1gqt | ACP | Ribokinase | / | 0.442 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.442 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.442 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.442 | |
| 2bx8 | AZQ | Serum albumin | / | 0.442 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3hwr | NDP | 2-dehydropantoate 2-reductase | / | 0.442 | |
| 3tdw | GDP | Gentamicin resistance protein | / | 0.442 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4jld | ADP | Adenylate kinase | / | 0.442 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.442 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 1i44 | ACP | Insulin receptor | 2.7.10.1 | 0.441 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1nq1 | 4HY | Thyroid hormone receptor beta | / | 0.441 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.441 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2i5b | ADP | Pyridoxine kinase | / | 0.441 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.441 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.441 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.441 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.441 | |
| 3pxv | FMN | Nitroreductase | / | 0.441 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4d81 | ADP | AAA ATPase, central domain protein | / | 0.441 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.441 | |
| 4ike | ADP | Adenylate kinase | / | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1qax | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.440 | |
| 2c96 | ATP | Psp operon transcriptional activator | / | 0.440 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.440 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.440 | |
| 4dlb | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.440 | |
| 4fmq | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.440 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.440 |