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 |
|---|---|---|---|
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 1.000 | |
| 3klm | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 1.000 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.537 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.520 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.515 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.484 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.482 | |
| 1osv | CHC | Bile acid receptor | / | 0.479 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.478 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.477 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.477 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.471 | |
| 1ouk | 084 | Mitogen-activated protein kinase 14 | / | 0.470 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.469 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.468 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.466 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.466 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.465 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.463 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.462 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.461 | |
| 1ppj | ANY | Cytochrome b | / | 0.460 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.459 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.458 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.458 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.458 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.457 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.457 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.457 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.457 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.456 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.455 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.455 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.454 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.454 | |
| 2ydw | WSH | Bromodomain-containing protein 2 | / | 0.453 | |
| 3gob | HXX | DdmC | / | 0.453 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.453 | |
| 4g73 | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.453 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.452 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.452 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.451 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.451 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.449 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.449 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.449 | |
| 2c6h | PXI | Cytochrome P450 monooxygenase PikC | / | 0.448 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.448 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.448 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.447 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.447 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.446 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.446 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.446 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.446 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4xxv | NAD | 3-isopropylmalate dehydrogenase | / | 0.446 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4iji | 99T | Glutathione S-transferase-like protein YibF | / | 0.445 | |
| 4v12 | POG | MaoC like domain protein | / | 0.445 | |
| 1q4x | G24 | Thyroid hormone receptor beta | / | 0.444 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.444 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.444 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.443 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3fl4 | FL4 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.443 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.443 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.442 | |
| 3lki | ATP | Fructokinase | / | 0.442 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.442 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.442 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.441 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.441 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.440 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.440 | |
| 4l8u | 9AZ | Serum albumin | / | 0.440 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.440 |