2WHF

Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines.

Podust, L.M.Ouellet, H.von Kries, J.P.de Montellano, P.R.

(2009) J Biol Chem 284: 25211-25219

  • DOI: 10.1074/jbc.M109.017632
  • Primary Citation of Related Structures:  
    2WH8, 2WGY, 2WHF

  • PubMed Abstract: 
  • The Mycobacterium tuberculosis P450 enzymes are of interest for their pharmacological development potential, as evidenced by their susceptibility to inhibition by antifungal azole drugs that normally target sterol 14alpha-demethylase (CYP51). Although antifungal azoles show promise, direct screening of compounds against M ...

    The Mycobacterium tuberculosis P450 enzymes are of interest for their pharmacological development potential, as evidenced by their susceptibility to inhibition by antifungal azole drugs that normally target sterol 14alpha-demethylase (CYP51). Although antifungal azoles show promise, direct screening of compounds against M. tuberculosis P450 enzymes may identify novel, more potent, and selective inhibitory scaffolds. Here we report that CYP130 from M. tuberculosis has a natural propensity to bind primary arylamines with particular chemical architectures. These compounds were identified via a high throughput screen of CYP130 with a library of synthetic organic molecules. As revealed by subsequent x-ray structure analysis, selected compounds bind in the active site by Fe-coordination and hydrogen bonding of the arylamine group to the carbonyl oxygen of Gly(243). As evidenced by the binding of structural analogs, the primary arylamine group is indispensable, but synergism due to hydrophobic contacts between the rest of the molecule and protein amino acid residues is responsible for a binding affinity comparable with that of the antifungal azole drugs. The topology of the CYP130 active site favors angular coordination of the arylamine group over the orthogonal coordination of azoles. Upon substitution of Gly(243) by an alanine, the binding mode of azoles and some arylamines reverted from type II to type I because of hydrophobic and steric interactions with the alanine side chain. We suggest a role for the conserved Ala(Gly)(243)-Gly(244) motif in the I-helix in modulating both the binding affinity of the axial water ligand and the ligand selectivity of cytochrome P450 enzymes.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE CYTOCHROME P450 130A413Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp130Rv1256cMTCY50.26
EC: 1.14
UniProt
Find proteins for P9WPN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPN5 
Go to UniProtKB:  P9WPN5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
II4 (Subject of Investigation/LOI)
Query on II4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]1-(3-METHYLPHENYL)-1H-BENZIMIDAZOL-5-AMINE
C14 H13 N3
VFSVFGIODYZMOF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
II4 BindingDB:  2WHF Kd: min: 4800, max: 3.26e+4 (nM) from 2 assay(s)
Binding MOAD:  2WHF Kd: 4800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.897α = 90
b = 53.942β = 96.73
c = 44.047γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.2: 2018-02-07
    Changes: Database references, Source and taxonomy