4GL7

Structure of human placental aromatase complexed with designed inhibitor HDDG046 (compound 5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel aromatase inhibitors by structure-guided design.

Ghosh, D.Lo, J.Morton, D.Valette, D.Xi, J.Griswold, J.Hubbell, S.Egbuta, C.Jiang, W.An, J.Davies, H.M.

(2012) J.Med.Chem. 55: 8464-8476

  • DOI: 10.1021/jm300930n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human cytochrome P450 aromatase catalyzes with high specificity the synthesis of estrogens from androgens. Aromatase inhibitors (AIs) such as exemestane, 6-methylideneandrosta-1,4-diene-3,17-dione, are preeminent drugs for the treatment of estrogen-d ...

    Human cytochrome P450 aromatase catalyzes with high specificity the synthesis of estrogens from androgens. Aromatase inhibitors (AIs) such as exemestane, 6-methylideneandrosta-1,4-diene-3,17-dione, are preeminent drugs for the treatment of estrogen-dependent breast cancer. The crystal structure of human placental aromatase has shown an androgen-specific active site. By utilization of the structural data, novel C6-substituted androsta-1,4-diene-3,17-dione inhibitors have been designed. Several of the C6-substituted 2-alkynyloxy compounds inhibit purified placental aromatase with IC(50) values in the nanomolar range. Antiproliferation studies in a MCF-7 breast cancer cell line demonstrate that some of these compounds have EC(50) values better than 1 nM, exceeding that for exemestane. X-ray structures of aromatase complexes of two potent compounds reveal that, per their design, the novel side groups protrude into the opening to the access channel unoccupied in the enzyme-substrate/exemestane complexes. The observed structure-activity relationship is borne out by the X-ray data. Structure-guided design permits utilization of the aromatase-specific interactions for the development of next generation AIs.


    Organizational Affiliation

    Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA. ghoshd@upstate.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 19A1
A
503Homo sapiensMutation(s): 0 
Gene Names: CYP19A1 (ARO1, CYAR, CYP19)
EC: 1.14.14.14
Find proteins for P11511 (Homo sapiens)
Go to Gene View: CYP19A1
Go to UniProtKB:  P11511
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
0XJ
Query on 0XJ

Download SDF File 
Download CCD File 
A
(6alpha,8alpha)-6-(pent-2-yn-1-yloxy)androsta-1,4-diene-3,17-dione
C24 H30 O3
VZGAHAQWKVTWEF-RAPVPNNWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0XJIC50: 11.8 - 12 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.445α = 90.00
b = 141.445β = 90.00
c = 118.851γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
CCP4phasing
REFMACrefinement
HKL-2000data scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-13 
  • Released Date: 2012-09-12 
  • Deposition Author(s): Ghosh, D.

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references
  • Version 1.2: 2012-10-24
    Type: Database references