1XUD

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1XUD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 

Literature

Structural basis for the highly selective inhibition of MMP-13.

Engel, C.K., Pirard, B., Schimanski, S., Kirsch, R., Habermann, J., Klingler, O., Schlotte, V., Weithmann, K.U., Wendt, K.U.

(2005) Chem Biol 12: 181-189

• PubMed: 15734640 
• DOI: https://doi.org/10.1016/j.chembiol.2005.01.008
• Primary Citation of Related Structures:  
  1XUD, 1XUR


• PubMed Abstract: 
  

  The paradigm for matrix metalloprotease inhibition combines active site tailoring and catalytic zinc ligation. But, selectivity has been difficult. Now, Engel et al. present novel compounds, completely selective for MMP-13, with a unique binding mode.

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Organizational Affiliation: 

Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880, USA

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.71 kDa 
• Atom Count: 3,208 
• Modelled Residue Count: 335 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	171	Homo sapiens	Mutation(s): 0  EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452  Go to UniProtKB:  P45452
PHAROS:  P45452 GTEx:  ENSG00000137745

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB4	G [auth A], L [auth B]	N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE C22 H20 F2 N4 O2 PYFRREJCFXFNRR-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PB4	PDBBind:  1XUD	IC50: 8 (nM) from 1 assay(s)
	BindingDB:  1XUD	IC50: min: 0.67, max: 110 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.022	α = 90
b = 36.475	β = 130.412
c = 95.06	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2005-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations