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 |
|---|---|---|---|
| 4fwn | AQP | Propionate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fwn | AQP | Propionate kinase | / | 1.000 | |
| 2e20 | B4P | Propionate kinase | / | 0.524 | |
| 2e1z | B4P | Propionate kinase | / | 0.517 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.497 | |
| 5c8d | 5AD | Probable transcriptional regulator | / | 0.485 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.478 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.477 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.476 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.475 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.473 | |
| 4z36 | ON3 | Lysophosphatidic acid receptor 1 | / | 0.472 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.471 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.470 | |
| 4de5 | 0JD | Pantothenate synthetase | 6.3.2.1 | 0.470 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.469 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 1q19 | SSC | Carbapenam-3-carboxylate synthase | 6.3.3.6 | 0.468 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.467 | |
| 3b4p | 3B4 | Phenazine biosynthesis protein A/B | / | 0.467 | |
| 3ebi | BEY | M1 family aminopeptidase | 3.4.11 | 0.465 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.465 | |
| 3dzl | 3OC | Phenazine biosynthesis protein A/B | / | 0.464 | |
| 4r09 | URI | Toll-like receptor 8 | / | 0.464 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.462 | |
| 3cl2 | G39 | Neuraminidase | / | 0.462 | |
| 3e9s | TTT | Replicase polyprotein 1ab | 3.4.22 | 0.462 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.462 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.461 | |
| 2xxv | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.461 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.461 | |
| 1x31 | FMN | Subunit alpha of sarocosine oxidase | / | 0.459 | |
| 1x31 | FMN | Subunit beta of sarcosine oxidase | / | 0.459 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.458 | |
| 3oe9 | ITD | C-X-C chemokine receptor type 4 | / | 0.458 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.457 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.457 | |
| 5c8a | 5AD | Probable transcriptional regulator | / | 0.457 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.456 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.456 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.456 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.455 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.455 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.455 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.454 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.454 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.454 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.454 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.454 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 3vd7 | GTZ | Beta-galactosidase | 3.2.1.23 | 0.454 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 2pja | 33Z | Carboxypeptidase B | / | 0.453 | |
| 3a5y | KAA | Elongation factor P--(R)-beta-lysine ligase | / | 0.453 | |
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 0.453 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.453 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.452 | |
| 4e2x | TYD | Methyltransferase | / | 0.452 | |
| 1i75 | NOJ | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.451 | |
| 1qvt | PRL | HTH-type transcriptional regulator QacR | / | 0.451 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.451 | |
| 1e6z | NGO | Chitinase | / | 0.450 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 2qxx | TTP | dCTP deaminase | 3.5.4.13 | 0.450 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 5hvn | NAD | 3-dehydroquinate synthase | / | 0.450 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 2ohm | 8AP | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3c8b | ARG_ARG_GLY_ILE_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.449 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.449 | |
| 5dn1 | AMZ | Phosphoribosyl isomerase A | 5.3.1.16 | 0.449 | |
| 1lvg | 5GP | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 5cuq | NSC | Genome polyprotein | / | 0.448 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.447 | |
| 2b1i | 93A | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.447 | |
| 2wca | NP6 | O-GlcNAcase BT_4395 | / | 0.447 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3v2y | ML5 | Sphingosine 1-phosphate receptor 1 | / | 0.447 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1v93 | FAD | Methylenetetrahydrofolate reductase | / | 0.446 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.446 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3p93 | KDG | D-galactonate dehydratase family member ManD | 4.2.1 | 0.446 | |
| 3ts1 | TYA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.446 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.445 | |
| 1tww | HH2 | Dihydropteroate synthase | / | 0.445 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.445 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 4ai8 | DZA | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.445 | |
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 0.444 | |
| 3ndj | JHZ | Methyltransferase | / | 0.444 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4gh1 | 0WX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.444 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.443 | |
| 1yro | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.443 | |
| 2dg3 | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2j41 | 5GP | Guanylate kinase | / | 0.443 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.443 | |
| 4iif | CTS | Beta-glucosidase 1 | 3.2.1.21 | 0.443 | |
| 1mc1 | PCX | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.442 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2qs4 | LY5 | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3vf2 | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.442 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.442 | |
| 4x7w | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 1ivs | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.441 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.441 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3fx6 | BPX | Carboxypeptidase A1 | 3.4.17.1 | 0.441 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1w6y | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.440 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.440 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.440 | |
| 4a1o | AMZ | Bifunctional purine biosynthesis protein PurH | 2.1.2.3 | 0.440 |