4G9L

Structure of MMP3 complexed with NNGH inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of matrix metalloproteinase-3 with a platinum-based inhibitor.

Belviso, B.D.Caliandro, R.Siliqi, D.Calderone, V.Arnesano, F.Natile, G.

(2013) Chem Commun (Camb) 49: 5492-5494

  • DOI: https://doi.org/10.1039/c3cc41278d
  • Primary Citation of Related Structures:  
    4DPE, 4G9L, 4JA1

  • PubMed Abstract: 

    An X-ray investigation has been performed with the aim of characterizing the binding sites of a platinum-based inhibitor (K[PtCl3(DMSO)]) of matrix metalloproteinase-3 (stromelysin-1). The platinum complex targets His224 in the S1' specificity loop, representing the first step in the selective inhibition process (PDB ID code 4JA1).


  • Organizational Affiliation

    Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stromelysin-1
A, B
173Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
PHAROS:  P08254
GTEx:  ENSG00000149968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08254
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGH
Query on NGH

Download Ideal Coordinates CCD File 
M [auth B]N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
C13 H20 N2 O5 S
JIRXORZYIXSWOB-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NGH BindingDB:  4G9L Ki: min: 132, max: 133 (nM) from 2 assay(s)
IC50: 6500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.99α = 90
b = 78.84β = 90
c = 106.73γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
ILMILIONEmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ILMILIONEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description