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 |
|---|---|---|---|
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 1.000 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.566 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.561 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.558 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.548 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.531 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.514 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.487 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.486 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.471 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.467 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.465 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.464 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.464 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.462 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.460 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.454 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.454 | |
| 1ysl | COA | Hydroxymethylglutaryl-CoA synthase | 2.3.3.10 | 0.453 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.452 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.450 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.450 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.450 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.448 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.448 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.447 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4n6b | COA | Uncharacterized protein | / | 0.447 | |
| 5dp2 | NAP | CurF | / | 0.447 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.446 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.444 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.443 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.443 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.443 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.442 | |
| 1zdw | FLV | Prenyltransferase | / | 0.442 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.442 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.442 | |
| 2hps | CTZ | Ca2+-triggered coelenterazine-binding protein 1 | / | 0.442 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.442 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.441 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.440 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.440 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3r96 | ACO | MccE protein | / | 0.440 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 |