1MZS

CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND dichlorobenzyloxy-indole-carboxylic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

First X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling

Daines, R.A.Pendrak, I.Sham, K.Van Aller, G.S.Konstantinidis, A.K.Lonsdale, J.T.Janson, C.A.Qiu, X.Brandt, M.Khandekar, S.S.Silverman, C.Head, M.S.

(2003) J Med Chem 46: 5-8

  • DOI: https://doi.org/10.1021/jm025571b
  • Primary Citation of Related Structures:  
    1MZS

  • PubMed Abstract: 

    The first cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor is reported. The inhibitor was obtained by rational modification of a high throughput screening lead with the aid of a S. pneumoniae FabH homology model. This homology model was used to design analogues that would have both high affinity for the enzyme and appropriate aqueous solubility to facilitate cocrystallization studies.


  • Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase III317Escherichia coliMutation(s): 1 
EC: 2.3.1.41
UniProt
Find proteins for P0A6R0 (Escherichia coli (strain K12))
Explore P0A6R0 
Go to UniProtKB:  P0A6R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6R0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
669
Query on 669

Download Ideal Coordinates CCD File 
C [auth A]1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
C22 H21 Cl2 N O5
JTGPYFFQVOIJKR-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
669 Binding MOAD:  1MZS IC50: 7000 (nM) from 1 assay(s)
PDBBind:  1MZS IC50: 7000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.34α = 90
b = 72.34β = 90
c = 100.73γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description