4GQL

Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470.1

Structural Biology Knowledgebase: 4GQL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.154
  • R-Value Work: 0.133

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GQL

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18684.81

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

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R47
Query on R47

A N-[(2S)-3-[(S)-(4-bromophenyl)(hydroxy)phosphoryl]- 2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol- 5-yl]methyl}propanoyl]-L-alpha-glutamyl-L- alpha-glutamine
RXP470.1 (Synonym)
C35 H35 Br Cl N4 O10 P
PTUCPHGSAFOJAU-MGONOCMRSA-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 %)
R47 N/A in BindingDB
Ki: 0.26 nM  BindingMOAD
Ki: 0.26 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.154
  • R-Value Work: 0.133
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.58 α = 90.00
b = 63.39 β = 90.00
c = 36.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-23
  • 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