5TH9

Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745 bound to MMP-9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biochemical characterization and structure determination of a potent, selective antibody inhibitor of human MMP9.

Appleby, T.C.Greenstein, A.E.Hung, M.Liclican, A.Velasquez, M.Villasenor, A.G.Wang, R.Wong, M.H.Liu, X.Papalia, G.A.Schultz, B.E.Sakowicz, R.Smith, V.Kwon, H.J.

(2017) J Biol Chem 292: 6810-6820

  • DOI: https://doi.org/10.1074/jbc.M116.760579
  • Primary Citation of Related Structures:  
    5TH6, 5TH9

  • PubMed Abstract: 

    Matrix metalloproteinase 9 (MMP9) is a member of a large family of proteases that are secreted as inactive zymogens. It is a key regulator of the extracellular matrix, involved in the degradation of various extracellular matrix proteins. MMP9 plays a pathological role in a variety of inflammatory and oncology disorders and has long been considered an attractive therapeutic target. GS-5745, a potent, highly selective humanized monoclonal antibody inhibitor of MMP9, has shown promise in treating ulcerative colitis and gastric cancer. Here we describe the crystal structure of GS-5745·MMP9 complex and biochemical studies to elucidate the mechanism of inhibition of MMP9 by GS-5745. GS-5745 binds MMP9 distal to the active site, near the junction between the prodomain and catalytic domain, and inhibits MMP9 by two mechanisms. Binding to pro-MMP9 prevents MMP9 activation, whereas binding to active MMP9 allosterically inhibits activity.


  • Organizational Affiliation

    From Gilead Sciences, Inc., Foster City, California 94404.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GS-5745 Fab light chainA [auth L],
D [auth M],
G [auth N]
214Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GS-5745 Fab heavy chainB [auth H],
E [auth I],
H [auth J]
230Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9,Matrix metalloproteinase-9C [auth A],
F [auth B],
I [auth C]
231Homo 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
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
N [auth A],
S [auth B],
X [auth C]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
O [auth B]
P [auth B]
T [auth C]
J [auth A],
K [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
L [auth A]
M [auth A]
Q [auth B]
R [auth B]
V [auth C]
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
V [auth C],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.167α = 90
b = 168.167β = 90
c = 234.735γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description