Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 37120.89 
• Atom Count: 2609 
• Residue Count: 318 
• Unique protein chains: 1

1UTZ

Crystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-yl)phenyl]-thien-2-yl}carboxamido)(phenyl)propanoic acid

• DOI: 10.2210/pdb1UTZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-12-12 Released: 2004-12-15 
• Deposition Author(s): Morales, R., Perrier, S., Florent, J.M., Beltra, J., Dufour, S., De Mendez, I., Manceau, P., Tertre, A., Moreau, F., Compere, D., Dublanchet, A.C., O'Gara, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 

Literature

Crystal Structures of Novel Non-Peptidic, Non-Zinc Chelating Inhibitors Bound to Mmp-12

Morales, R., Perrier, S., Florent, J.M., Beltra, J., Dufour, S., De Mendez, I., Manceau, P., Tertre, A., Moreau, F., Compere, D., Dublanchet, A.C., O'Gara, M.

(2004) J.Mol.Biol. 341: 1063

• PubMed: 15289103 
• DOI: 10.1016/j.jmb.2004.06.039
• Primary Citation of Related Structures:  
  1UTT, 1ROS
• Also Cited By: 3DPF, 3DPE, 3DNG


• PubMed Abstract: 
  

Human macrophage elastase (MMP-12) plays an important role in inflammatory processes and has been implicated in diseases such as emphysema and chronic obstructive pulmonary disease (COPD). It is therefore an attractive target for therapeutic agents. As part of a structure-based drug design programme to find new inhibitors of MMP-12, the crystal structures of the MMP-12 catalytic domain (residues 106-268) complexed to three different non-peptidic small molecule inhibitors have been determined. The structures reveal that all three ligands bind in the S1' pocket but show varying degrees of interaction with the Zn atom. The structures of the complexes with inhibitors CP-271485 and PF-00356231 reveal that their central morpholinone and thiophene rings, respectively, sit over the Zn atom at a distance of approximately 5A, locating the inhibitors halfway down the S1' pocket. In both of these structures, an acetohydroxamate anion, an artefact of the crystallisation solution, chelates the zinc atom. By contrast, the acetohydroxamate anion is displaced by the ligand in the structure of MMP-12 complexed to PD-0359601 (Bayer), a potent zinc chelating N-substituted biaryl butyric acid, used as a reference compound for crystallisation. Although a racemate was used for the crystallisation, the S enantiomer only is bound in the crystal. Important hydrophobic interactions between the inhibitors and residues from the S1' pocket are observed in all of the structures. The relative selectivity displayed by these ligands for MMP-12 over other MMP family members is discussed.

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Organizational Affiliation: 

Pfizer Global Research and Development, Fresnes Laboratories, 94265 Fresnes Cedex, France [corrected]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MACROPHAGE METALLOELASTASE	A, B	159	Homo sapiens	Mutation(s): 0  Gene Names: MMP12 (HME) EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens) Go to Gene View: MMP12 Go to UniProtKB:  P39900

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HAE	A, B	ACETOHYDROXAMIC ACID C2 H5 N O2 RRUDCFGSUDOHDG-UHFFFAOYSA-N
PF3	A, B	(2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL}CARBOXAMIDO)(PHENYL)PROPANOIC ACID PF-00356231; 3-PHENYL-3-({[4-(4-PYRIDIN-4-YLPHENYL)THIEN-2-YL]CARBONYL}AMINO)PROPANOIC ACID C25 H20 N2 O3 S VMTJQZUZINLEKC-JOCHJYFZSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PF3	IC50: 14 nM (100) BINDINGDB
PF3	IC50: 14 nM BINDINGMOAD
PF3	IC50: 1400 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 
• Space Group: P 6₃ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 123.224	α = 90.00
b = 123.224	β = 90.00
c = 168.200	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
CNX	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-12 
• Released Date: 2004-12-15 
• Deposition Author(s): Morales, R., Perrier, S., Florent, J.M., Beltra, J., Dufour, S., De Mendez, I., Manceau, P., Tertre, A., Moreau, F., Compere, D., Dublanchet, A.C., O'Gara, M.

Revision History 

• Version 1.0: 2004-12-15
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-05-08
  Type: Data collection, Experimental preparation, Other