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 |
|---|---|---|---|
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 1.000 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.565 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.555 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.554 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.517 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.515 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.514 | |
| 1ysl | COA | Hydroxymethylglutaryl-CoA synthase | 2.3.3.10 | 0.486 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.485 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.483 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.477 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.476 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.473 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.471 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.468 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.468 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.466 | |
| 5cts | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.466 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.462 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.462 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.462 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.462 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.461 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.461 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.460 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.458 | |
| 2fa3 | ACO | Hydroxymethylglutaryl-CoA synthase | / | 0.457 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.457 | |
| 3eks | CY9 | Actin-5C | / | 0.457 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.454 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 3r95 | ACO | MccE protein | / | 0.454 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.453 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.453 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.453 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.453 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.452 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.452 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.452 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 1zdw | FLV | Prenyltransferase | / | 0.451 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.450 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.450 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.450 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.449 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.449 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.449 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.449 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.448 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.448 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.447 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.447 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 3eku | CY9 | Actin-5C | / | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.446 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.446 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.445 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.445 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.445 | |
| 1csc | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.444 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.444 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.444 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.444 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.444 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.443 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.442 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.441 | |
| 3zuy | TCH | Transporter | / | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.441 | |
| 4pmj | NAP | Putative oxidoreductase | / | 0.441 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.441 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 3r96 | ACO | MccE protein | / | 0.440 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.440 |