4GR3

Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470A

Structural Biology Knowledgebase: 4GR3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 4GR3

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18574.29

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: catalytic domain (UNP residues 106-263)
Mutation: F171D
Gene Name(s): MMP12 Gene View HME
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R45
Query on R45

A N-{(2S)-3-[(S)-(4-bromophenyl)(hydroxy)phosphoryl]- 2-[(3-phenyl-1,2-oxazol-5-yl)methyl]propanoyl}- L-alpha-glutamyl-L-alpha-glutamine
RXP470A (Synonym)
C29 H32 Br N4 O10 P
RXBMEHOLQJITJI-LEOXJPRUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
R45 N/A in BindingDB
Ki: 15.5 nM  BindingMOAD
Ki: 15.5 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.180
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.96 α = 90.00
b = 63.13 β = 90.00
c = 37.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-24
  • Released Date: 2013-02-06
  • Deposition author(s): Stura, E.A., Vera, L., Beau, F., Devel, L., Cassar-Lajeunesse, E., Dive, V.

Revision History

  • 2013-05-22
    Type: Citation | Details: Citation update