2OVX

MMP-9 active site mutant with barbiturate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 2OVX

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 37508.25

Macromolecule Entities
Molecule Chains Length Organism Details
Matrix metalloproteinase-9 (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB) A, B 159 Homo sapiens EC#: 3.4.24.35 IUBMB
Fragment: CATALYTIC DOMAIN RESIDUES: 110-215, 391-443
Mutation: E402Q
Gene Name(s): MMP9 Gene View CLG4B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4MR
Query on 4MR

A, B 5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN-2-YLPIPERAZIN- 1-YL)PYRIMIDINE-2,4,6(2H,3H)-TRIONE
C24 H22 N6 O4
FMKQJGOROFNCGM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4MR N/A in BindingDB
N/A in BindingMoad
IC50: 2 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.217
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 55.23 α = 90.00
b = 55.23 β = 90.00
c = 259.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-15
  • Released Date: 2007-06-19
  • Deposition author(s): Tochowicz, A., Bode, W., Maskos, K., Goettig, P.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance
  • 2017-08-16
    Type: Advisory, Source and taxonomy