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 |
|---|---|---|---|
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 1.000 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.631 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.595 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.521 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.485 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.479 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.478 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.478 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.470 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.468 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.464 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.464 | |
| 4lb2 | DM5 | Serum albumin | / | 0.464 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.463 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.462 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.460 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.460 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.460 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.459 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.458 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.457 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.457 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.454 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.454 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4fv3 | EK6 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.452 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.452 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.451 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.450 | |
| 3a3g | DLZ | Lumazine protein | / | 0.450 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.450 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.450 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.449 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.449 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.448 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.448 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.448 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.447 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.445 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.445 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.445 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.444 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.444 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.444 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 3gob | HXX | DdmC | / | 0.444 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.444 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.444 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.443 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.443 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.443 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.443 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.443 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.443 | |
| 4zca | ADP | Kinesin-like protein KIF11 | / | 0.443 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.442 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.442 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.442 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.442 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1q41 | IXM | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.441 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.441 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.441 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.441 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4fsm | HK1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.441 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3p0j | TYE | Putative tyrosyl-tRNA synthetase | / | 0.440 |