sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2aib | ERG | Beta-elicitin cinnamomin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2aib | ERG | Beta-elicitin cinnamomin | / | 1.000 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.667 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.510 | |
| 1osv | CHC | Bile acid receptor | / | 0.489 | |
| 4pd6 | URI | Nucleoside permease | / | 0.483 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.479 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 2y03 | Y01 | Beta-1 adrenergic receptor | / | 0.477 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.477 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.476 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 3stu | DK3 | Methylketone synthase I | / | 0.474 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.471 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.468 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.468 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.468 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.467 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.466 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.466 | |
| 2y00 | Y01 | Beta-1 adrenergic receptor | / | 0.464 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.464 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.463 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.463 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.462 | |
| 2y02 | Y01 | Beta-1 adrenergic receptor | / | 0.461 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 3ict | COA | Coenzyme A disulfide reductase | / | 0.460 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.460 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.460 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.460 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.458 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.458 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.458 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.457 | |
| 2ayl | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.457 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.456 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.456 | |
| 3f5p | 741 | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.456 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.456 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.455 | |
| 3n8w | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.455 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.454 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.454 | |
| 4feh | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.454 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.454 | |
| 3sh0 | SAX | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.453 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.452 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.451 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.451 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.451 | |
| 4ez7 | 2AN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.451 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 4pds | ANP | Serine/threonine-protein kinase RAD53 | 2.7.12.1 | 0.451 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.451 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.450 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.450 | |
| 3l8p | 0CE | Angiopoietin-1 receptor | 2.7.10.1 | 0.450 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.450 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.450 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.450 | |
| 1d3g | BRE | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.449 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.449 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.449 | |
| 2jd0 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.449 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.449 | |
| 3abi | NAD | Uncharacterized protein | / | 0.449 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.449 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.449 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.449 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.449 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.448 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3bzu | A21 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.448 | |
| 5br4 | NAD | Lactaldehyde reductase | 1.1.1.77 | 0.448 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.447 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 2y01 | Y01 | Beta-1 adrenergic receptor | / | 0.447 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.447 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.447 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.447 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.446 | |
| 3kk6 | CEL | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.446 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.446 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.446 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.445 | |
| 1fbm | RTL | Cartilage oligomeric matrix protein | / | 0.445 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.445 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.445 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.445 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3lu8 | IQX | Serum albumin | / | 0.444 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 3wec | AUI | Cytochrome P450 | / | 0.444 | |
| 4bqu | CLR | Japanin | / | 0.444 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.444 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.443 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.443 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.442 | |
| 2oye | IM8 | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.442 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.442 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.442 | |
| 3w18 | N13 | Aurora kinase A | 2.7.11.1 | 0.442 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.441 | |
| 2c0i | L1G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.441 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.441 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.441 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 5a3c | NAD | SIR2 family protein | / | 0.441 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.441 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.440 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.440 |