4GL5

Structure of human placental aromatase complexed with designed inhibitor HDDG029 (compound 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 
    0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted G29Click on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1021/jm300930n
  • Primary Citation of Related Structures:  
    3S79, 3S7S, 4GL5, 4GL7

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 19A1503Homo sapiensMutation(s): 0 
EC: 1.14.14.1 (PDB Primary Data), 1.14.14.14 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11511 (Homo sapiens)
Explore P11511 
Go to UniProtKB:  P11511
PHAROS:  P11511
GTEx:  ENSG00000137869 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11511
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
G29
Query on G29

Download Ideal Coordinates CCD File 
C [auth A](6alpha,8alpha)-6-(but-2-yn-1-yloxy)androsta-1,4-diene-3,17-dione
C23 H28 O3
GNDYBZKXORBCFO-KVAKACLVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G29 BindingDB:  4GL5 IC50: 112.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.329α = 90
b = 140.329β = 90
c = 118.733γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted G29Click on this verticalbar to view details

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2012-10-24
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations