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 |
|---|---|---|---|
| 3nt4 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3nt4 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 1.000 | |
| 3nt2 | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.637 | |
| 3nt5 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.627 | |
| 4l8v | NAP | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.564 | |
| 3ec7 | NAD | Inositol 2-dehydrogenase | / | 0.559 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.536 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.515 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.504 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.499 | |
| 1psd | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.492 | |
| 5agl | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.490 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.485 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.479 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.479 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.479 | |
| 3in9 | H1S | Heparin lyase I | / | 0.478 | |
| 3ntq | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.478 | |
| 3jta | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.476 | |
| 3m2t | NAD | Probable dehydrogenase | / | 0.476 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 3px2 | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.473 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.473 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.471 | |
| 1mdl | SMN | Mandelate racemase | / | 0.470 | |
| 3c9s | ACP | Thiamine-monophosphate kinase | / | 0.470 | |
| 3o9z | NAD | Lipopolysaccaride biosynthesis protein wbpB | / | 0.470 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.469 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 3jt4 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.468 | |
| 5agk | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.468 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.467 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 4xd1 | T3Q | Qdtf | / | 0.467 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.466 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.464 | |
| 3jt3 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.464 | |
| 3jt6 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.464 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.463 | |
| 3q9a | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.463 | |
| 1mdl | RMN | Mandelate racemase | / | 0.462 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.462 | |
| 1evj | NAD | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.460 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.460 | |
| 2ga9 | AGS | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.459 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.458 | |
| 2cmk | CDP | Cytidylate kinase | 2.7.4.25 | 0.458 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.458 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.458 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.457 | |
| 4qvb | F42 | F420H(2)-dependent reductase Rv1155 | 1.4.3.5 | 0.457 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.456 | |
| 2jgb | MGT | Eukaryotic translation initiation factor 4E type 2 | / | 0.456 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.456 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 3t58 | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.456 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.456 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.456 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.455 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.455 | |
| 5brp | PNG | Glycoside Hydrolase Family 13 | / | 0.455 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.454 | |
| 2ay9 | 5PV | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.454 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2wwj | Y28 | Lysine-specific demethylase 4A | / | 0.454 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.453 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.453 | |
| 3vax | PLP | Uncharacterized protein | / | 0.453 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.453 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2e1z | B4P | Propionate kinase | / | 0.452 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.452 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.452 | |
| 3pzc | GAP | Amino acid--[acyl-carrier-protein] ligase 1 | 6.2.1.n2 | 0.452 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.452 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1orr | CDP | CDP-paratose 2-epimerase | / | 0.451 | |
| 5fmm | MGT | Polymerase basic protein 2 | / | 0.451 | |
| 1o5i | NAD | 3-oxoacyl-(Acyl carrier protein) reductase | / | 0.450 | |
| 1ryd | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.450 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 2q0g | UPU | Poly(A) polymerase, putative | / | 0.450 | |
| 3av7 | KYN | Uncharacterized protein | / | 0.450 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.450 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.450 | |
| 3v2u | ATP | Protein GAL3 | / | 0.450 | |
| 4u0o | MTA | Lipoyl synthase 2 | / | 0.450 | |
| 2wtk | ANP | STE20-related kinase adapter protein alpha | / | 0.449 | |
| 1h6a | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.448 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2lbv | EB4 | Extracellular fatty acid-binding protein | / | 0.448 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.448 | |
| 4iix | 1EG | Microcin C7 self-immunity protein MccF | / | 0.448 | |
| 4nzo | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.448 | |
| 4o7n | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 | 0.448 | |
| 5dt9 | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.448 | |
| 1arh | PPD | Aspartate aminotransferase | 2.6.1.1 | 0.447 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.447 | |
| 1zzr | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.447 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.447 | |
| 3hgg | CHD | CmeR | / | 0.447 | |
| 3qh2 | 3NM | Thiazole tautomerase | / | 0.447 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.447 | |
| 4rpj | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.447 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.447 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.446 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.446 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.446 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.446 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.446 | |
| 4koa | NDP | 1,5-anhydro-D-fructose reductase | 1.1.1.292 | 0.446 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.446 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1mk1 | APR | MutT/nudix family protein | / | 0.445 | |
| 1nb6 | UTP | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.445 | |
| 2b9j | ADP | Mitogen-activated protein kinase FUS3 | 2.7.11.24 | 0.445 | |
| 2e77 | FMN | Lactate oxidase | / | 0.445 | |
| 2pa3 | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.445 | |
| 3hf3 | FMN | Chromate reductase | / | 0.445 | |
| 3px3 | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.445 | |
| 3srz | UPG | Toxin A | / | 0.445 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.445 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.444 | |
| 1gir | NDP | Iota toxin component Ia | / | 0.444 | |
| 1h6b | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.444 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.444 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.444 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.444 | |
| 5a02 | NAP | Glucose-fructose oxidoreductase | / | 0.444 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.443 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.443 | |
| 2x3j | ATP | AcsD | / | 0.443 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.443 | |
| 2cul | FAD | GidA-related protein | / | 0.442 | |
| 3pfh | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.442 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.442 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.442 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.441 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.441 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.441 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.441 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.441 | |
| 3nh8 | DC2 | N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming) | 3.5.1.114 | 0.441 | |
| 4itm | ATP | Tetraacyldisaccharide 4'-kinase | / | 0.441 | |
| 4m2a | UPG | UDP-glucose pyrophosphorylase | / | 0.441 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.441 | |
| 5a05 | NDP | Glucose-fructose oxidoreductase | / | 0.441 | |
| 5eg3 | ACP | Fibroblast growth factor receptor 2 | / | 0.441 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.440 | |
| 1o04 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.440 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3ele | PLP | Aminotransferase | / | 0.440 | |
| 3fuf | BES | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3tfp | 03L | Dehydrosqualene synthase | / | 0.440 | |
| 4xcz | T3Q | Qdtf | / | 0.440 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.440 | |
| 5a04 | NDP | Glucose-fructose oxidoreductase | / | 0.440 |