2W09

CYP51 OF M. TUBERCULOSIS BOUND TO AN INHIBITOR CIS-4-METHYL-N-[(1S)-3-(METHYLSULFANYL)-1-(PYRIDIN-4-YLCARBAMOYL)PROPYL]CYCLOHEXANECARBOXAMIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Trypanosoma Cruzi Cyp51 Inhibitor Derived from a Mycobacterium Tuberculosis Screen Hit.

Chen, C.-K., Doyle, P.S., Yermalitskaya, L.V., Mackey, Z.B., Ang, K.K.H., Mckerrow, J.H., Podust, L.M.

(2009) PLoS Negl Trop Dis 3: E372

  • DOI: https://doi.org/10.1371/journal.pntd.0000372
  • Primary Citation of Related Structures:  
    2W09, 2W0A, 2W0B

  • PubMed Abstract: 

    The two front-line drugs for chronic Trypanosoma cruzi infections are limited by adverse side-effects and declining efficacy. One potential new target for Chagas' disease chemotherapy is sterol 14alpha-demethylase (CYP51), a cytochrome P450 enzyme involved in biosynthesis of membrane sterols.

    • Organizational Affiliation: 

    Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME P450 51455Mycobacterium tuberculosis H37RvMutation(s): 2 
EC: 1.14.13.70
UniProt
Find proteins for P9WPP9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP9 
Go to UniProtKB:  P9WPP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP9
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
CM9
Query on CM9
Download Ideal Coordinates CCD File 
C [auth A]CIS-4-METHYL-N-[(1S)-3-(METHYLSULFANYL)-1-(PYRIDIN-4-YLCARBAMOYL)PROPYL]CYCLOHEXANECARBOXAMIDE
C18 H27 N3 O2 S
OCZKGSPGDOPDAI-LZWOXQAQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CM9 Binding MOAD:  2W09 Kd: 3.54e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.436α = 90
b = 85.162β = 90
c = 110.944γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2009-01-20 
    • Deposition Author(s): Podust, L.M.

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description