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 |
|---|---|---|---|
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 1.000 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.627 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.590 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.576 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.561 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.557 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.543 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.534 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.532 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.530 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.528 | |
| 2aqb | TL6 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.527 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.507 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.500 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.491 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.490 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.488 | |
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.476 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.476 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.474 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.470 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.469 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.469 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.467 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.465 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.463 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.463 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.460 | |
| 5dp2 | NAP | CurF | / | 0.459 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.458 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.455 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.455 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.451 | |
| 4boe | CLR | Japanin | / | 0.451 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.451 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.450 | |
| 3ha7 | B32 | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.449 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.448 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.448 | |
| 2g0b | NLT | Long-chain N-acyl amino acid synthase | / | 0.447 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.447 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.447 | |
| 4j7h | TRH | PCZA361.3 | / | 0.447 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.447 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.446 | |
| 4e2y | JHZ | Methyltransferase | / | 0.446 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.446 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.445 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.443 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.443 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.443 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.442 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.441 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.440 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.440 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.440 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |