3ELM

Crystal Structure of MMP-13 Complexed with Inhibitor 24f


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.164

Literature

Macromolecules
Sequence Display for 3ELM

Classification: HYDROLASE

Total Structure Weight: 40034.20

Macromolecule Entities
Molecule Chains Length Organism Details
Collagenase 3 A, B 171 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: UNP residues 104 to 274
Gene Name(s): MMP13 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
24F
Query on 24F

A, B (2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1- [(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid
C23 H30 N2 O7 S2
GYETWAWIKBOMPE-OAQYLSRUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
24F IC50: 0.5 nM (100) BindingDB
Ki: 0.19 nM (100) BindingDB

IC50: 0.5 nM  BindingMOAD
Ki: 0.19 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.164
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 134.50 α = 90.00
b = 36.07 β = 130.53
c = 95.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-22
  • Released Date: 2009-07-21
  • Deposition author(s): Kulathila, R., Monovich, L., Koehn, J.

Revision History

  • 2011-07-13
    Type: Version format compliance