3I7I

MMP-13 in complex with a non zinc-chelating inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.208 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors.

Heim-Riether, A.Taylor, S.J.Liang, S.Gao, D.A.Xiong, Z.Michael August, E.Collins, B.K.Farmer, B.T.Haverty, K.Hill-Drzewi, M.Junker, H.D.Mariana Margarit, S.Moss, N.Neumann, T.Proudfoot, J.R.Keenan, L.S.Sekul, R.Zhang, Q.Li, J.Farrow, N.A.

(2009) Bioorg.Med.Chem.Lett. 19: 5321-5324

  • DOI: 10.1016/j.bmcl.2009.07.151
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published ...

    Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1' pocket.


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals, Department of Medicinal Chemistry, 900 Ridgebury Rd, Ridgefield, CT 06877, USA. alexander.heim-riether@boehringer-ingelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
171Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
518
Query on 518

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Download CCD File 
A
N-[4-(5-{[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]carbamoyl}furan-2-yl)phenyl]-1-benzofuran-2-carboxamide
C29 H29 N3 O5
JFDVHGPZDKQUGQ-SANMLTNESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
518IC50: 620 nM (100) BINDINGDB
518IC50: 620 nM BINDINGMOAD
518IC50: 620 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.208 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.186α = 90.00
b = 35.777β = 131.08
c = 95.295γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance