2YIG

MMP13 in complex with a novel selective non zinc binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Selective Non Zinc Binding Inhibitors of Mmp13.

Savi, C.D.Morley, A.D.Ting, A.Nash, I.Karabelas, K.Wood, C.M.James, M.Norris, S.J.Karoutchi, G.Rankine, N.Hamlin, G.Macfaul, P.A.Ryan, D.Baker, S.V.Hargreaves, D.Gerhardt, S.

(2011) Bioorg Med Chem Lett 21: 4215

  • DOI: https://doi.org/10.1016/j.bmcl.2011.05.075
  • Primary Citation of Related Structures:  
    2YIG

  • PubMed Abstract: 

    Directed screening has identified a novel series of MMP13 inhibitors that possess good levels of activity whilst possessing excellent selectivity over related MMPs. The binding mode of the series has been solved by co-crystallisation and demonstrates an interesting mode of inhibition without interaction with the catalytic zinc atom.


  • Organizational Affiliation

    AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COLLAGENASE 3
A, B
171Homo sapiensMutation(s): 0 
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5EL
Query on 5EL

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO[2.2.2]OCT-3-YL]ETHYNYL}PHENOXY)-N-(PYRIDIN-4-YLMETHYL)BENZAMIDE
C28 H27 N3 O3
FEOIBPWKGPFSTB-NDEPHWFRSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5EL BindingDB:  2YIG IC50: min: 79, max: 125.89 (nM) from 3 assay(s)
PDBBind:  2YIG IC50: 79.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.417α = 90
b = 36.074β = 131.49
c = 95.206γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other