7XGJ

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 4.0 of the entry. See complete history


Literature

Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis.

Takeuchi, T.Hayashi, M.Tamita, T.Nomura, Y.Kojima, N.Mitani, A.Takeda, T.Hitaka, K.Kato, Y.Kamitani, M.Mima, M.Toki, H.Ohkubo, M.Nozoe, A.Kakinuma, H.

(2022) J Med Chem 65: 8493-8510

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00613
  • Primary Citation of Related Structures:  
    7XGJ, 7XJO

  • PubMed Abstract: 

    Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase that plays important roles in the degradation of extracellular matrix proteins. MMP2 is considered to be an attractive target for the treatment of various diseases such as cancer, arthritis, and fibrosis. In this study, we have developed a novel class of MMP2-selective inhibitors by hybridizing the peptide that binds to a zinc ion and S2-S5 pockets with small molecules that bind to the S1' pocket. Structural modifications based on X-ray crystallography revealed that the introduction of 2,4-diaminobutanoic acid (Dab) at position 4 dramatically enhanced MMP2 selectivity by forming an electrostatic interaction with Glu130. After improving the metabolic and chemical stability, TP0556351 ( 9 ) was identified. It exhibited potent MMP2 inhibitory activity (IC 50 = 0.20 nM) and extremely high selectivity. It suppressed the accumulation of collagen in a bleomycin-induced idiopathic pulmonary fibrosis model in mice, demonstrating the efficacy of MMP2-selective inhibitors for fibrosis.


  • Organizational Affiliation

    Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-2
A, B, C
168Homo sapiensMutation(s): 0 
Gene Names: MMP2
EC: 3.4.24.24
UniProt & NIH Common Fund Data Resources
Find proteins for P08253 (Homo sapiens)
Explore P08253 
Go to UniProtKB:  P08253
PHAROS:  P08253
GTEx:  ENSG00000087245 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08253
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GZS-ASN-ASP-ALA-LEU-IML-EOE-NH2
D, E, F
8Iris severe mosaic virusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
O [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
IML
Query on IML
D, E, F
L-PEPTIDE LINKINGC7 H15 N O2ILE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.831α = 90
b = 41.305β = 96.06
c = 92.467γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 2.0: 2022-07-13
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2023-04-05
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 4.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations