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 |
|---|---|---|---|
| 1a4r | GNH | Cell division control protein 42 homolog |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1a4r | GNH | Cell division control protein 42 homolog | / | 1.000 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.489 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.479 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.476 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.475 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.474 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.473 | |
| 1sny | NAP | LD36273p | / | 0.472 | |
| 4itr | GDP | Cell division control protein 42 homolog | / | 0.472 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.471 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.470 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.470 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.470 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.469 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.468 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.468 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.467 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.467 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.464 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.462 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.462 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.462 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.461 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 3zm5 | IGM | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.461 | |
| 1jmi | UMP | Thymidylate synthase | / | 0.460 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.460 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.460 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.459 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.459 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.459 | |
| 1tys | TMP | Thymidylate synthase | / | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.456 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.456 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.456 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.456 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.455 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.455 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.455 | |
| 1gvw | 0EM | Endothiapepsin | 3.4.23.22 | 0.454 | |
| 1kny | APC | Kanamycin nucleotidyltransferase | 2.7.7 | 0.454 | |
| 3a3g | DLZ | Lumazine protein | / | 0.454 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.454 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 4i42 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.454 | |
| 5dp2 | NAP | CurF | / | 0.454 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.453 | |
| 3o3p | GDD | Glycosyl transferase, family 2 | / | 0.453 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.453 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.452 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.452 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.452 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.451 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.451 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.450 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.450 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.450 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.450 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.448 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.448 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.448 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.448 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.448 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.448 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.448 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.448 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.447 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.447 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.447 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.447 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.447 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2jjj | 0QS | Endothiapepsin | 3.4.23.22 | 0.446 | |
| 2yvg | NAD | Ferredoxin reductase | / | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.446 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.445 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.445 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.445 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2nua | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.445 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.445 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.445 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.445 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.444 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.444 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.443 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 3eku | CY9 | Actin-5C | / | 0.443 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.443 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.442 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.442 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.442 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.442 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.442 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.442 | |
| 3wcz | NAP | Aldo-keto reductase AKR2E4 | / | 0.442 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.442 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1jmg | UMP | Thymidylate synthase | / | 0.441 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1qvn | FRI | Interleukin-2 | / | 0.441 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.441 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.441 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.441 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.441 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.441 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.441 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.440 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.440 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.440 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.440 | |
| 3prs | RIT | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.440 |