|Entry||Database: PDB / ID: 4gl5|
|Title||Structure of human placental aromatase complexed with designed inhibitor HDDG029 (compound 4)|
|Components||Cytochrome P450 19A1|
|Keywords||Oxidoreductase/Oxidoreductase Inhibitor / Oxidoreductase / Estrogen synthetase / Cytochrome P450 reductase / ER membrane / Oxidoreductase-Oxidoreductase Inhibitor complex|
|Function / homology|
Function and homology information
aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / negative regulation of macrophage chemotaxis / mammary gland development / steroid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / steroid hydroxylase activity / aromatase activity / female gonad development / uterus development / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-G29 / PROTOPORPHYRIN IX CONTAINING FE / Aromatase
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.48 Å|
|Citation||Journal: J.Med.Chem. / Year: 2012|
Title: Novel aromatase inhibitors by structure-guided design.
Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M.
|Structure viewer||Molecule: |
Downloads & links
A: Cytochrome P450 19A1
|#1: Protein|| |
Mass: 57954.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P11511, unspecific monooxygenase
|#2: Chemical|| ChemComp-HEM / |
|#3: Chemical|| ChemComp-G29 / (|
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 5.82 Å3/Da / Density % sol: 78.88 %|
|Crystal grow||Temperature: 277 K / Method: vapor diffusion / pH: 7.4 |
Details: The enzyme-inhibitor complexes were prepared by the addition from 20mM stock solutions of compound 4 in PEG550 to 18 M (~1mg/ml) of aromatase, to give a final inhibitor concentration of 300 ...Details: The enzyme-inhibitor complexes were prepared by the addition from 20mM stock solutions of compound 4 in PEG550 to 18 M (~1mg/ml) of aromatase, to give a final inhibitor concentration of 300 uM. The mixture was incubated overnight at 4 C in 100mM potassium phosphate buffer pH 7.4 containing 20% glycerol, 20mM dithiothreitol, 0.5 M ASD and 1mM BDM. The complex was then concentrated to 25-30mg/ml using ultrafiltration. Protein was setup for crystallization using protein to cocktail ratios 2:1 and 3:1. The protein was mixed with reservoir cocktails of 24-30% polyethylene glycol 4000 in 50mM NaCl, 50mM Tris, pH 8.5 and vapor diffused in sealed 24-well sitting drop plates against corresponding reservoir solution., VAPOR DIFFUSION, temperature 277K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å|
|Detector||Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2009|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.979 Å / Relative weight: 1|
|Reflection||Resolution: 3.48→121.53 Å / Num. all: 17289 / Num. obs: 17289 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 14.1|
|Refinement||Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.48→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.88 / SU B: 21.02 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.368 / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS|
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK|
|Displacement parameters||Biso mean: 91.221 Å2|
|Refinement step||Cycle: LAST / Resolution: 3.48→50 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 3.48→3.571 Å / Total num. of bins used: 20 |
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