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 |
|---|---|---|---|
| 3gco | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gco | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 1.000 | |
| 3gcn | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.627 | |
| 3gds | VAL_TYR_TYR_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.501 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.495 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.480 | |
| 3gdv | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.479 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 2r3y | VAL_TYR_TRP_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.477 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.475 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.473 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.472 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.468 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.466 | |
| 3gc8 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.466 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.465 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.465 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.464 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.464 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.464 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.463 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.461 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.461 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.461 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.460 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.458 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.458 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.458 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.457 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 1rbm | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.455 | |
| 2wpw | ACO | Orf14 | / | 0.455 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.455 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.454 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.453 | |
| 1gqt | ACP | Ribokinase | / | 0.453 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.453 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.452 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.452 | |
| 2y3r | TRK | TamL | / | 0.452 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.452 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.451 | |
| 4dpm | COA | Malonyl-CoA reductase | 1.2.1.75 | 0.451 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.450 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.449 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.449 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.447 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.447 | |
| 4a32 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bew | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.447 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.447 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.446 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.446 | |
| 3wdl | ATP | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.446 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.445 | |
| 3gdu | TYR_ARG_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.445 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.445 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.445 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.444 | |
| 3nwy | GTP | Uridylate kinase | / | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.443 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.443 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.443 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.443 | |
| 1nde | MON | Estrogen receptor beta | / | 0.442 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.442 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.442 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.442 | |
| 4i2q | 1BT | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.441 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.440 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.440 | |
| 4em9 | TCE | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.440 |