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 |
|---|---|---|---|
| 1kt4 | RTL | Retinol-binding protein 4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1kt4 | RTL | Retinol-binding protein 4 | / | 1.000 | |
| 1kt7 | RTL | Retinol-binding protein 4 | / | 0.736 | |
| 1aqb | RTL | Retinol-binding protein 4 | / | 0.656 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.648 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.622 | |
| 1iiu | RTL | Retinol-binding protein 4 | / | 0.609 | |
| 1brp | RTL | Retinol-binding protein 4 | / | 0.590 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.587 | |
| 1osv | CHC | Bile acid receptor | / | 0.515 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.510 | |
| 3fmz | 2T1 | Retinol-binding protein 4 | / | 0.495 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.494 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.488 | |
| 1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.482 | |
| 1kt5 | RTL | Retinol-binding protein 4 | / | 0.482 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.479 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.479 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.477 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.477 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.474 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.473 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.473 | |
| 4pd6 | URI | Nucleoside permease | / | 0.473 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.470 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.470 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.466 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.466 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 1sqi | 869 | 4-hydroxyphenylpyruvate dioxygenase | / | 0.465 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.465 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.465 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.464 | |
| 4rrx | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.464 | |
| 5dg3 | U21 | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | / | 0.464 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.462 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.462 | |
| 4hxy | NDP | Plm1 | / | 0.462 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.460 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.460 | |
| 5a3b | APR | SIR2 family protein | / | 0.460 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.459 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 2fhk | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.456 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.455 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.455 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.454 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.454 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.454 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.454 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.453 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.453 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.453 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.453 | |
| 4qij | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.453 | |
| 5ag7 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.453 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.452 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.451 | |
| 4a32 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.451 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.451 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.450 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.450 | |
| 4feh | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.450 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.450 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.449 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.449 | |
| 2wpx | ACO | Orf14 | / | 0.449 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.448 | |
| 3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.448 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.448 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.448 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.447 | |
| 2r04 | W71 | Genome polyprotein | / | 0.447 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.447 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4kao | KAO | Focal adhesion kinase 1 | 2.7.10.2 | 0.447 | |
| 5dt0 | SKE | Aurora kinase A | 2.7.11.1 | 0.447 | |
| 1geu | NAD | Glutathione reductase | 1.8.1.7 | 0.446 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2qu6 | 857 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.446 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3ntg | D72 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 5ag5 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.445 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.445 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 2p15 | EZT | Estrogen receptor | / | 0.445 | |
| 3dtw | A96 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.445 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 4kov | KOV | Uncharacterized protein | / | 0.445 | |
| 4li7 | 1XP | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.445 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.444 | |
| 4z35 | ON9 | Lysophosphatidic acid receptor 1 | / | 0.444 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.443 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.443 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.443 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.443 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.443 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.442 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.442 | |
| 2nmt | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.442 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.442 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.442 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.442 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4bqu | CLR | Japanin | / | 0.442 | |
| 4iqq | D16 | Thymidylate synthase | / | 0.442 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.441 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.441 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.441 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.441 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.441 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.441 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.440 | |
| 1tys | DHF | Thymidylate synthase | / | 0.440 | |
| 1v5e | FAD | Pyruvate oxidase | / | 0.440 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3aba | FLI | Cytochrome P450 | / | 0.440 | |
| 3ang | DCC | Transcriptional repressor, TetR family | / | 0.440 | |
| 3bhr | THG | Thymidylate synthase | / | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4b1f | KRH | Glutamate racemase | / | 0.440 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.440 |