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 |
|---|---|---|---|
| 3rgf | BAX | Cyclin-dependent kinase 8 | 2.7.11.22 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3rgf | BAX | Cyclin-dependent kinase 8 | 2.7.11.22 | 1.000 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.494 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.487 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.486 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.484 | |
| 1iep | STI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.482 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.482 | |
| 4eyj | N61 | Mitogen-activated protein kinase 13 | 2.7.11.24 | 0.480 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.477 | |
| 3vhk | BPK | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.475 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.472 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.472 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.471 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.470 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.470 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.469 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.468 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.466 | |
| 1ysx | 4EB | Serum albumin | / | 0.465 | |
| 3vnt | 0JA | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.465 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.465 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.465 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.464 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.464 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.464 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.463 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 3efl | 706 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.463 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.461 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.460 | |
| 1xqc | AEJ | Estrogen receptor | / | 0.460 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.460 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.460 | |
| 3vs1 | VSA | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.460 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.459 | |
| 1sqv | UHD | Cytochrome b | / | 0.458 | |
| 2ewp | TXF | Estrogen-related receptor gamma | / | 0.458 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.458 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.458 | |
| 5bvw | 1N1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.458 | |
| 5doz | NDP | JamJ | / | 0.458 | |
| 1osv | CHC | Bile acid receptor | / | 0.457 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.457 | |
| 4qrc | 0LI | Fibroblast growth factor receptor 4 | 2.7.10.1 | 0.457 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.456 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.456 | |
| 2ic3 | HBY | Gag-Pol polyprotein | 2.7.7.49 | 0.456 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.456 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.456 | |
| 3w8z | HTK | Putative FAD-dependent oxygenase EncM | / | 0.456 | |
| 4i2q | 1BT | Gag-Pol polyprotein | 2.7.7.49 | 0.456 | |
| 1hk1 | T44 | Serum albumin | / | 0.455 | |
| 2oiq | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.455 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.455 | |
| 3zbn | COA | 3-ketoacyl-CoA thiolase-like protein | / | 0.455 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.455 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.455 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.455 | |
| 5hi2 | BAX | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.455 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.455 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2uvy | GVI | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 3gcs | BAX | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4hia | FMN | LOV protein | / | 0.454 | |
| 3cxh | SMA | Cytochrome b | / | 0.453 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3h1j | SMA | Cytochrome b | / | 0.453 | |
| 3u2l | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.453 | |
| 4l98 | LRG | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.452 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.452 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.452 | |
| 3gwn | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.452 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3m8c | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.452 | |
| 4at5 | MUJ | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.452 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 4ucn | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.452 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3ffi | 3OB | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.450 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.450 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.450 | |
| 3vs4 | VSF | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.450 | |
| 4em9 | TCE | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2c0t | L3G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.449 | |
| 4ase | AV9 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.449 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.449 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.448 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3kq7 | KQ7 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.448 | |
| 4iah | 1DX | Alr2278 protein | / | 0.448 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.448 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.448 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.448 | |
| 1hih | C20 | Gag-Pol polyprotein | / | 0.447 | |
| 1xp6 | AIU | Estrogen receptor | / | 0.447 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 3nbp | JGZ | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.447 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.447 | |
| 4nfh | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1cx2 | S58 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
| 1e94 | ANP | ATP-dependent protease ATPase subunit HslU | / | 0.446 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.446 | |
| 1wbw | LI4 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 2yix | YIX | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4c2j | COA | 3-ketoacyl-CoA thiolase, mitochondrial | 2.3.1.16 | 0.446 | |
| 4iae | 1DX | Alr2278 protein | / | 0.446 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.445 | |
| 2jdv | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2jg7 | NAD | Antiquitin | / | 0.445 | |
| 2vv9 | IM9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.445 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 3hv5 | R24 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.445 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4y9x | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.445 | |
| 1ezv | SMA | Cytochrome b | / | 0.444 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.444 | |
| 1rrm | APR | Lactaldehyde reductase | 1.1.1.77 | 0.444 | |
| 2qjy | SMA | Cytochrome b | / | 0.444 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.444 | |
| 3gki | CLR | Niemann-Pick C1 protein | / | 0.444 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.444 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3oct | 1N1 | Tyrosine-protein kinase BTK | 2.7.10.2 | 0.444 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4af3 | VX6 | Aurora kinase B | 2.7.11.1 | 0.444 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.443 | |
| 2nmt | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.443 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 4o2z | 046 | Mitogen-activated protein kinase | / | 0.443 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.442 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.442 | |
| 2ibz | SMA | Cytochrome b | / | 0.442 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3amb | VX6 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 3mfr | ANP | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 4agw | NG7 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.442 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4ksp | 1SU | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.442 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 5a28 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.441 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.441 | |
| 1kyo | SMA | Cytochrome b | / | 0.441 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.441 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 2y37 | A54 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.441 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3otq | MZL | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.441 | |
| 4m8e | 29V | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.441 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.441 | |
| 1e1l | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.440 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.440 | |
| 1kb9 | SMA | Cytochrome b | / | 0.440 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.440 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.440 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.440 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.440 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3lu6 | IMX | Serum albumin | / | 0.440 | |
| 3qlf | PD5 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.440 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4dym | IYZ | Activin receptor type-1 | 2.7.11.30 | 0.440 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.440 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.440 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.440 |