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 |
|---|---|---|---|
| 4jtz | 1NW | Genome polyprotein | 2.7.7.48 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4jtz | 1NW | Genome polyprotein | 2.7.7.48 | 1.000 | |
| 4ju6 | 1O6 | Genome polyprotein | 2.7.7.48 | 0.661 | |
| 4ju7 | 1O6 | Genome polyprotein | 2.7.7.48 | 0.661 | |
| 4ju3 | 1O1 | Genome polyprotein | 2.7.7.48 | 0.574 | |
| 2hwh | RNA | Genome polyprotein | 2.7.7.48 | 0.545 | |
| 4eo8 | 0S3 | Genome polyprotein | 2.7.7.48 | 0.526 | |
| 2gir | NN3 | Genome polyprotein | 2.7.7.48 | 0.513 | |
| 4jju | 1MB | Genome polyprotein | 2.7.7.48 | 0.501 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 4ju4 | 1O3 | Genome polyprotein | 2.7.7.48 | 0.477 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.477 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.476 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.473 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.471 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.471 | |
| 3cxh | SMA | Cytochrome b | / | 0.468 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.467 | |
| 3mf5 | HJZ | Genome polyprotein | 2.7.7.48 | 0.465 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.465 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.464 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.463 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.463 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.462 | |
| 3h1j | SMA | Cytochrome b | / | 0.462 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.462 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.462 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.461 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.461 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.460 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.460 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.460 | |
| 1d3g | BRE | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.459 | |
| 1kyo | SMA | Cytochrome b | / | 0.459 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.459 | |
| 2jd1 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.459 | |
| 2qfx | NDP | Isocitrate dehydrogenase [NADP], mitochondrial | 1.1.1.42 | 0.459 | |
| 2qjy | SMA | Cytochrome b | / | 0.459 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.459 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.459 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.459 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.459 | |
| 1ezv | SMA | Cytochrome b | / | 0.458 | |
| 4k11 | 0J9 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.458 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.457 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.456 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.455 | |
| 1osv | CHC | Bile acid receptor | / | 0.454 | |
| 3u1y | 03I | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.454 | |
| 3vhk | BPK | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 4z44 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.454 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.453 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.453 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.453 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.452 | |
| 1ybg | TAV | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.452 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.452 | |
| 2yiu | SMA | Cytochrome b | / | 0.452 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.452 | |
| 3w2c | N15 | Aurora kinase A | 2.7.11.1 | 0.452 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.451 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.451 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.450 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.450 | |
| 3lan | KBT | Gag-Pol polyprotein | 2.7.7.49 | 0.450 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.450 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.450 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.449 | |
| 2jd0 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.449 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.448 | |
| 1kb9 | SMA | Cytochrome b | / | 0.448 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.448 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.448 | |
| 3cx5 | SMA | Cytochrome b | / | 0.448 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.447 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.446 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.446 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.446 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.446 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.446 | |
| 2o3z | AI7 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.446 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 3l8p | 0CE | Angiopoietin-1 receptor | 2.7.10.1 | 0.446 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.446 | |
| 4oze | 24G | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.446 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.446 | |
| 5ajq | DB8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.446 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.445 | |
| 3bhl | THG | Thymidylate synthase | / | 0.445 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.445 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.445 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.445 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.444 | |
| 2ibz | SMA | Cytochrome b | / | 0.444 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.444 | |
| 2y03 | Y01 | Beta-1 adrenergic receptor | / | 0.444 | |
| 2y30 | SM8 | Putative repressor SimReg2 | / | 0.444 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.444 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.444 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.444 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.444 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.444 | |
| 1f28 | F89 | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1nde | MON | Estrogen receptor beta | / | 0.443 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.443 | |
| 1pp9 | SMA | Cytochrome b | / | 0.443 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.443 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.443 | |
| 3dtw | A96 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.443 | |
| 4c4h | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.443 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.443 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.442 | |
| 1zhz | ERG | Oxysterol-binding protein homolog 4 | / | 0.442 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.442 | |
| 3aba | FLI | Cytochrome P450 | / | 0.442 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4c4f | 7CE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.442 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.442 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.441 | |
| 1qvn | FRI | Interleukin-2 | / | 0.441 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.441 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.441 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.441 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.441 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.441 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.441 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.441 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3bej | MUF | Bile acid receptor | / | 0.440 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.440 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.440 | |
| 3vrz | VRZ | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 3vs5 | VSG | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 4a4w | YFB | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4h4o | 506 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.440 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.440 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.440 |