7WXX | pdb_00007wxx

Crystal structure of human MMP-7 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors by Hybridizing the S1' Subsite Binder with Short Peptides.

Tabuse, H.Abe-Sato, K.Kanazawa, H.Yashiro, M.Tamura, Y.Kamitani, M.Hitaka, K.Gunji, E.Mitani, A.Kojima, N.Oka, Y.

(2022) J Med Chem 65: 13253-13263

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01088
  • Primary Citation Related Structures: 
    7WXX

  • PubMed Abstract: 

    Matrix metalloproteinase-7 (MMP-7) has emerged as a protein playing important roles in both physiological and pathophysiological processes. Despite the growing interest in MMP-7 as a potential therapeutic target for diseases including cancer and fibrosis, potent and selective MMP-7 inhibitors have yet to be identified. Compound 1 , previously reported by Edman and co-workers, binds to the S1' subsite of MMP-7, exhibiting moderate inhibitory activity and selectivity. To achieve both higher inhibitory activity and selectivity, we conceived hybridizing 1 with short peptides. The initially designed compound 6 , which was a hybrid molecule between 1 and a tripeptide (Ala-Leu-Met) derived from an MMP-2-inhibitory peptide (APP-IP), showed enhanced MMP-7-inhibitory activity. Subsequent optimization of the peptide moiety led to the development of compound 18 with remarkable potency for MMP-7 and selectivity over other MMP subtypes.


  • Organizational Affiliation
    • Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan.

Macromolecule Content 

  • Total Structure Weight: 20.32 kDa 
  • Atom Count: 1,520 
  • Modeled Residue Count: 171 
  • Deposited Residue Count: 182 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Matrilysin175Homo sapiensMutation(s): 1 
Gene Names: MMP7MPSL1PUMP1
EC: 3.4.24.23
UniProt & NIH Common Fund Data Resources
Find proteins for P09237 (Homo sapiens)
Explore P09237 
Go to UniProtKB:  P09237
PHAROS:  P09237
GTEx:  ENSG00000137673 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09237
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide Inhibitor7synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.36α = 90
b = 77.36β = 90
c = 62.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Refinement description