4GR8

Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470C

Structural Biology Knowledgebase: 4GR8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GR8

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 17742.35

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A 152 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: catalytic domain (UNP residues 111-262)
Mutation: F171D
Gene Name(s): MMP12 Gene View HME
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R4C
Query on R4C

A N-{(2S)-3-[(R)-(4-bromophenyl)(hydroxy)phosphoryl]- 2-[(3-phenyl-1,2-oxazol-5-yl)methyl]propanoyl}- L-alanyl-L-alaninamide
RXP470C (Synonym)
C25 H28 Br N4 O6 P
HXHLWPVBBLIGJV-XYJFISCASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
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 %)
R4C N/A in BindingDB
Ki: 14.7 nM  BindingMOAD
Ki: 14.7 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000868 (ALA,NH2,14E) A N-{(2S)-3-[(R)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-[(3-PHENYL-1,2-OXAZOL-5-YL)METHYL]PROPANOYL}-L-ALANYL-L-ALANINAMIDE Peptide-like /
Enzyme inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.177
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.83 α = 90.00
b = 61.47 β = 90.00
c = 33.46 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