3DPE

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor

Structural Biology Knowledgebase: 3DPE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DPE

Classification: HYDROLASE

Total Structure Weight: 18862.40

Macromolecule Entities
Molecule Chains Length Organism Details
Neutrophil collagenase A 163 Homo sapiens EC#: 3.4.24.34 IUBMB
Fragment: MMP-8 catalytic domain, UNP residues 100-262
Gene Name(s): MMP8 Gene View CLG1

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

A N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)- 1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}- 4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3- d]pyrimidine-2-carboxamide 7,7-dioxide
C24 H21 N5 O6 S2
QHDIXGPUTSAIJX-UHFFFAOYSA-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 %)
AXB IC50: 57 nM (100) BindingDB

IC50: 57 nM  BindingMOAD
IC50: 57 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.210
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 32.29 α = 90.00
b = 68.95 β = 105.41
c = 32.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-08
  • Released Date: 2009-03-03
  • Deposition author(s): Pochetti, G., Montanari, R., Mazza, F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4