Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.54 kDa 
• Atom Count: 1303 
• Residue Count: 161 
• Unique protein chains: 1

2JT6

Solution structure of matrix metalloproteinase 3 (MMP-3) in the presence of 3-4'-cyanobyphenyl-4-yloxy)-n-hdydroxypropionamide (MMP-3 inhibitor VII)

• DOI: 10.2210/pdb2JT6/pdb
• BMRB: 15396

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-23 Released: 2008-02-19 
• Deposition Author(s): Alcaraz, L.A., Banci, L., Bertini, I., Cantini, F., Donaire, A., Gonnelli, L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 

Literature

Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors

Alcaraz, L.A., Banci, L., Bertini, I., Cantini, F., Donaire, A., Gonnelli, L.

(2007) J Biol Inorg Chem 12: 1197-1206

• PubMed: 17710450 
• DOI: 10.1007/s00775-007-0288-9
• Primary Citation of Related Structures:  
  2JNP, 2JT6, 2JT5


• PubMed Abstract: 
  

We structurally characterized the adducts of the catalytic domain of matrix metalloproteinase-3 (MMP3) with three different nonpeptidic inhibitors by solving the solution structure of one adduct [MMP3-N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid] and then by calculating structural models of the other two adducts using a reduced set of experimental NMR data, following a recently proposed procedure (Bertini et al. in J. Med. Chem. 48:7544-7559, 2005). The inhibitors were selected with the criteria of maintaining in all of them the same zinc-coordinating moiety and of selectively changing the substituents and/or the functional groups. The backbone dynamics on various time scales have been characterized as well. The comparison among these structures and with others previously reported allowed us to elucidate fine details of inhibitor-receptor interactions and to develop some criteria, which could guide in optimizing the design of selective inhibitors.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromelysin-1	A	161	Homo sapiens	Mutation(s): 0  Gene Names: MMP3, STMY1 EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens) Explore P08254  Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS:  P08254 GTEx:  ENSG00000149968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JT6	A	3-[(4'-cyanobiphenyl-4-yl)oxy]-N-hydroxypropanamide C16 H14 N2 O3 XZWFHJUEAVOHHG-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JT6	Ki :  25   nM  PDBBind
JT6	Kd:  100   nM  BindingDB
JT6	IC50:  47   nM  BindingDB
JT6	IC50:  25   nM  BindingDB
JT6	Kd:  110   nM  BindingDB
JT6	IC50:  57   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2JT6 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-23 
• Released Date: 2008-02-19 
Deposition Author(s): Alcaraz, L.A., Banci, L., Bertini, I., Cantini, F., Donaire, A., Gonnelli, L.

Revision History 

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-02-19
  Changes: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Other