1XUC

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

Structural Biology Knowledgebase: 1XUC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XUC

Classification: Hydrolase

Total Structure Weight: 39641.80

Macromolecule Entities
Molecule Chains Length Organism Details
Collagenase 3 A, B 171 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: Catalytic domain
Gene Name(s): MMP13 Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PB3
Query on PB3

A, B N,N'-BIS(3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE
PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-(3-METHYL- BENZYLAMIDE) (Synonym)
C22 H22 N4 O2
GTBUZLPQANSGGE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PB3 IC50: 72 nM (100) BindingDB

IC50: 72 nM  BindingMOAD
IC50: 72 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.175
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 134.44 α = 90.00
b = 36.48 β = 130.51
c = 95.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-26
  • Released Date: 2005-10-26
  • Deposition author(s): Engel, C.K., Wendt, K.U.

Revision History

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