3PKC

M. tuberculosis MetAP with bengamide analog Y08, in Mn form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.

Lu, J.P.Yuan, X.H.Yuan, H.Wang, W.L.Wan, B.Franzblau, S.G.Ye, Q.Z.

(2011) Chemmedchem 6: 1041-1048

  • DOI: 10.1002/cmdc.201100003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine aminopeptidase (MetAP) carries out an essential function of protein N-terminal processing in many bacteria and is a promising target for the development of novel antitubercular agents. Natural bengamides potently inhibit the proliferation ...

    Methionine aminopeptidase (MetAP) carries out an essential function of protein N-terminal processing in many bacteria and is a promising target for the development of novel antitubercular agents. Natural bengamides potently inhibit the proliferation of mammalian cells by targeting MetAP enzymes, and the X-ray crystal structure of human type 2 MetAP in complex with a bengamide derivative reveals the key interactions at the active site. By preserving the interactions with the conserved residues inside the binding pocket while exploring the differences between bacterial and human MetAPs around the binding pocket, seven bengamide derivatives were synthesized and evaluated for inhibition of MtMetAP1a and MtMetAP1c in different metalloforms, inhibition of M. tuberculosis growth in replicating and non-replicating states, and inhibition of human K562 cell growth. Potent inhibition of MtMetAP1a and MtMetAP1c and modest growth inhibition of M. tuberculosis were observed for some of these derivatives. Crystal structures of MtMetAP1c in complex with two of the derivatives provided valuable structural information for improvement of these inhibitors for potency and selectivity.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase
A
285Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: map (mapB)
EC: 3.4.11.18
Find proteins for P9WK19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WK19
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Y08
Query on Y08

Download SDF File 
Download CCD File 
A
(E,2R,3R,4S,5R)-N-[[(3S)-1-cyclopropylcarbonylpiperidin-3-yl]methyl]-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
C22 H38 N2 O6
JFNUXOSYQRHRBI-NNURDPEKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y08IC50: 960 nM BINDINGMOAD
Y08IC50: 960 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.667α = 90.00
b = 79.945β = 91.80
c = 65.055γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
SCALEPACKdata scaling
HKL-3000data reduction
DENZOdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-11-11 
  • Released Date: 2011-04-20 
  • Deposition Author(s): Ye, Q.Z., Lu, J.P.

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description