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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

View Full Validation Report



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