8K4Z | pdb_00008k4z

Crystal structure of human MMP-7 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.218 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8K4Z

This is version 1.1 of the entry. See complete history

Literature

Discovery of TP0628103: A Highly Potent and Selective MMP-7 Inhibitor with Reduced OATP-Mediated Clearance Designed by Shifting Isoelectric Points.

Oka, Y.Abe-Sato, K.Tabuse, H.Yasukawa, Y.Yahara, T.Nishimoto, T.Kamitani, M.Fukunaga, T.Ochiai, N.Kumasaka-Abe, T.Hitaka, K.Gunji, E.Ohara, H.Takeda, T.Kojima, N.Asami, T.

(2024) J Med Chem 67: 1406-1420

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01967
  • Primary Citation Related Structures: 
    8K4Z

  • PubMed Abstract: 

    Matrix metalloproteinase-7 (MMP-7) has been shown to play an important role in pathophysiological processes such as cancer and fibrosis. We previously discovered selective MMP-7 inhibitors by molecular hybridization and structure-based drug design. However, the systemic clearance (CL tot ) of the biologically active lead compound was very high. Because our studies revealed that hepatic uptake by organic anion transporting polypeptide (OATP) was responsible for the high CL tot , we found a novel approach to reducing their uptake based on isoelectric point (IP) values as an indicator for substrate recognition by OATP1B1/1B3. Our "IP shift strategy" to adjust the IP values culminated in the discovery of TP0628103 ( 18 ), which is characterized by reduced in vitro OATP-mediated hepatic uptake and in vivo CL tot . Our in vitro - in vivo extrapolation of OATP-mediated clearance and the "IP shift strategy" provide crucial insights for a new medicinal chemistry approach to reducing the systemic clearance of OATP1B1/1B3 substrates.


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

Macromolecule Content 

  • Total Structure Weight: 20.55 kDa 
  • Atom Count: 1,409 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 181 
  • 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
Inhibitor6synthetic constructMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
G [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
N9P
Query on N9P
B
L-PEPTIDE LINKINGC8 H10 N2 O2ALA
TBG
Query on TBG
B
L-PEPTIDE LINKINGC6 H13 N O2VAL

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.218 (DCC) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.799α = 90
b = 75.799β = 90
c = 60.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata 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: 2024-04-17
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references, Structure summary