8K5V

Crystal structure of human proMMP-9 catalytic domain in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


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Literature

Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation.

Nishikawa-Shimono, R.Kuwabara, M.Fujisaki, S.Matsuda, D.Endo, M.Kamitani, M.Futamura, A.Nomura, Y.Yamaguchi-Sasaki, T.Yabuuchi, T.Yamaguchi, C.Tanaka-Yamamoto, N.Satake, S.Abe-Sato, K.Funayama, K.Sakata, M.Takahashi, S.Hirano, K.Fukunaga, T.Uozumi, Y.Kato, S.Tamura, Y.Nakamori, T.Mima, M.Mishima-Tsumagari, C.Nozawa, D.Imai, Y.Asami, T.

(2023) Bioorg Med Chem Lett 97: 129541-129541

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129541
  • Primary Citation of Related Structures:  
    8K5V, 8K5W, 8K5X, 8K5Y

  • PubMed Abstract: 

    Matrix metalloproteinase-9 (MMP-9) is a secreted zinc-dependent endopeptidase that degrades the extracellular matrix and basement membrane of neurons, and then contributes to synaptic plasticity by remodeling the extracellular matrix. Inhibition of MMP-9 activity has therapeutic potential for neurodegenerative diseases such as fragile X syndrome. This paper reports the molecular design, synthesis, and in vitro studies of novel indole derivatives as inhibitors of proMMP-9 activation. High-throughput screening (HTS) of our internal compound library and subsequent merging of hit compounds 1 and 2 provided compound 4 as a bona-fide lead. X-ray structure-based design and subsequent lead optimization led to the discovery of compound 33, a highly potent and selective inhibitor of proMMP-9 activation.


  • Organizational Affiliation

    Medicinal Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9
A, B
242Homo sapiensMutation(s): 0 
Gene Names: MMP9CLG4B
EC: 3.4.24.35
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
PHAROS:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VOC (Subject of Investigation/LOI)
Query on VOC

Download Ideal Coordinates CCD File 
H [auth A]6,7-dihydro-4H-[1,3]oxazolo[4,5-c]pyridin-5-yl-(7-ethyl-2H-indazol-3-yl)methanone
C16 H16 N4 O2
JCOAMLYFOYJAMQ-UHFFFAOYSA-N
2HP
Query on 2HP

Download Ideal Coordinates CCD File 
N [auth B]DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.04α = 90
b = 73.82β = 104.21
c = 77.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release