3I7G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    3I7G, 3I7I

  • 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 MMP-13 inhibitors ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagenase 3A, B171Homo sapiensMutation(s): 0 
Gene Names: MMP13
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
732
Query on 732

Download Ideal Coordinates CCD File 
I [auth A]5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide
C20 H23 Cl N2 O3
SOSADZXKACRLDA-SFHVURJKSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
732 Binding MOAD:  3I7G IC50: 430 (nM) from 1 assay(s)
BindingDB:  3I7G IC50: 430 (nM) from 1 assay(s)
PDBBind:  3I7G IC50: 430 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.77α = 90
b = 36.1β = 130.77
c = 95.333γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2009-07-08 
  • Released Date: 2009-09-01 
  • Deposition Author(s): Farrow, N.A.

Revision History  (Full details and data files)

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