4GR0

Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470B

Structural Biology Knowledgebase: 4GR0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GR0

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18568.76

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
R4B
Query on R4B

A N-[(2S)-3-[(R)-(4-bromophenyl)(hydroxy)phosphoryl]- 2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol- 5-yl]methyl}propanoyl]-L-alanyl-L-alaninamide
RXP470B (Synonym)
C31 H31 Br Cl N4 O6 P
LIUMDGLYGBIKBM-SFYKDHMMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
R4B N/A in BindingDB
Ki: 0.28 nM  BindingMOAD
Ki: 0.28 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.186
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.77 α = 90.00
b = 62.76 β = 90.00
c = 37.84 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