Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 18.57 kDa 
• Atom Count: 1545 
• Modelled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

4GR0

Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470B

• PDB DOI: 10.2210/pdb4GR0/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-08-24 Released: 2013-02-06 
• Deposition Author(s): Stura, E.A., Vera, L., Beau, F., Devel, L., Cassar-Lajeunesse, E., Dive, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Molecular determinants of a selective matrix metalloprotease-12 inhibitor: insights from crystallography and thermodynamic studies.

Czarny, B., Stura, E.A., Devel, L., Vera, L., Cassar-Lajeunesse, E., Beau, F., Calderone, V., Fragai, M., Luchinat, C., Dive, V.

(2013) J Med Chem 56: 1149-1159

• PubMed: 23343195 
• DOI: 10.1021/jm301574d
• Primary Citation of Related Structures:  
  4GQL, 4GR0, 4GR3, 4GR8


• PubMed Abstract: 
  

The molecular determinants responsible for the potency of the RXP470.1 phosphinic peptide inhibitor toward matrix metalloprotease-12 (MMP-12) remain elusive. To address this issue, structure-activity study, X-ray crystallography, and isothermal titration calorimetry (ITC) experiments were performed. The crystal structure of MMP-12/inhibitor complex (1.15 Å) reveals that the inhibitor establishes multiple interactions with the MMP-12 active site, with its long P(1)' side chain filling most of the S(1)' deep cavity. ITC experiments indicate that the binding of this inhibitor to MMP-12 is mostly entropy driven (ΔG° = -13.1 kcal/mol, ΔH° = -2.53 kcal/mol, and -TΔS° = -10.60 kcal/mol) and involves a proton uptake from the buffer. Comparing phosphinic versus hydroxamate inhibitors reveals that the chelation of the zinc ion is slightly different, leading the inhibitor backbone to adopt a position in which the hydrogen bonding with the MMP-12 active site is less favorable in phosphinic inhibitor while maintaining high affinity.

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Organizational Affiliation: 

CEA, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191 Cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	159	Homo sapiens	Mutation(s): 1  Gene Names: HME, MMP12 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R4B	G [auth A]	N-[(2S)-3-[(R)-(4-bromophenyl)(hydroxy)phosphoryl]-2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]methyl}propanoyl]-L-a lanyl-L-alaninamide C31 H31 Br Cl N4 O6 P LIUMDGLYGBIKBM-SFYKDHMMSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
R4B	Binding MOAD:  4GR0	Ki: 0.28 (nM) from 1 assay(s)
	BindingDB:  4GR0	Ki: 0.28 (nM) from 1 assay(s)
	PDBBind:  4GR0	Ki: 0.28 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000865 (R4B)	G [auth A]	N-[(2S)-3-[(R)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}PROPANOYL]-L-ALANYL-L-ALANINAMIDE	Peptide-like / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.77	α = 90
b = 62.76	β = 90
c = 37.84	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-24 
• Released Date: 2013-02-06 
Deposition Author(s): Stura, E.A., Vera, L., Beau, F., Devel, L., Cassar-Lajeunesse, E., Dive, V.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references