1G4K

X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.244

Literature

Macromolecules
Sequence Display for 1G4K

Classification: HYDROLASE

Total Structure Weight: 58437.64

Macromolecule Entities
Molecule Chains Length Organism Details
STROMELYSIN-1 A, B, C 168 Homo sapiens EC#: 3.4.24.17 IUBMB
Fragment: CATALYTIC DOMAIN
Gene Name(s): MMP3 Gene View STMY1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C 5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE- 2,4,6-TRIONE
C17 H14 N2 O4
RTBMLCLTYAPKIF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HQQ IC50: 2000 nM (100) BindingDB

N/A in BindingMoad
IC50: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.244
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.80 α = 90.00
b = 103.80 β = 90.00
c = 147.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-10-27
  • Released Date: 2001-04-25
  • Deposition author(s): Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4