2WO8

MMP12 complex with a beta hydroxy carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Identification of Beta-Hydroxy Carboxylic Acids as Selective Mmp-12 Inhibitors.

Holmes, I.P.Gaines, S.Watson, S.P.Lorthioir, O.Walker, A.Baddeley, S.J.Herbert, S.Egan, D.Convery, M.A.Singh, O.M.P.Gross, J.W.Strelow, J.M.Smith, R.H.Amour, A.J.Brown, D.Martin, S.L.

(2009) Bioorg Med Chem Lett 19: 5760

  • DOI: 10.1016/j.bmcl.2009.07.155
  • Primary Citation of Related Structures:  
    2WOA, 2WO8, 2WO9

  • PubMed Abstract: 
  • A new class of selective MMP-12 inhibitors have been identified via high throughput screening. Crystallization with MMP-12 confirmed the mode of binding and allowed initial optimization to be carried out using classical structure based design.


    Organizational Affiliation

    GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MACROPHAGE METALLOELASTASE ABCD164Homo sapiensMutation(s): 0 
Gene Names: MMP12HME
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
NIH Common Fund Data Resources
PHAROS:  P39900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
023
Query on 023

Download Ideal Coordinates CCD File 
B, D
N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDROXY)AMINO]ETHYL}-5-PHENYLPENTANOYL]-N,3-DIMETHYL-L-VALINAMIDE
C21 H33 N3 O4
GHVMTHKJUAOZJP-CGTJXYLNSA-N
 Ligand Interaction
077
Query on 077

Download Ideal Coordinates CCD File 
A, C
(3S)-5-biphenyl-4-yl-3-hydroxypentanoic acid
C17 H18 O3
ILGSIIFHQGOKKV-INIZCTEOSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
077IC50:  520   nM  Binding MOAD
77IC50 :  520   nM  PDBBind
077IC50:  520   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.043α = 66.47
b = 65.264β = 83.86
c = 67.808γ = 71.37
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance