Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.78 kDa 
• Atom Count: 2798 
• Residue Count: 342 
• Unique protein chains: 1

1D8F

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A PIPERAZINE BASED INHIBITOR.

• DOI: 10.2210/pdb1D8F/pdb

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


• Deposited: 1999-10-22 Released: 2000-10-23 
• Deposition Author(s): Cheng, M.Y., De, B., Pikul, S., Almstead, N.G., Natchus, M.G., Anastasio, M.V., McPhail, S.J., Snider, C.E., Taiwo, Y.O., Chen, L.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.294 

Literature

Design and synthesis of piperazine-based matrix metalloproteinase inhibitors.

Cheng, M., De, B., Pikul, S., Almstead, N.G., Natchus, M.G., Anastasio, M.V., McPhail, S.J., Snider, C.E., Taiwo, Y.O., Chen, L., Dunaway, C.M., Gu, F., Dowty, M.E., Mieling, G.E., Janusz, M.J., Wang-Weigand, S.

(2000) J Med Chem 43: 369-380

• PubMed: 10669564 
• DOI: 10.1021/jm990366q
• Primary Citation of Related Structures:  
  1D8F


• PubMed Abstract: 
  

A new generation of cyclic matrix metalloproteinase (MMP) inhibitors derived from dl-piperazinecarboxylic acid has been described. The design involves: incorporation of hydroxamic acid as the bidentate chelating agent for catalytic Zn(2+), placement of a sulfonamide group at the 1N-position of the piperazine ring to fill the S1' pocket of the enzyme, and finally attachment of diverse functional groups at the 4N-position to optimize potency and peroral absorption. A unique combination of all three elements produced inhibitor 20 with high affinity for MMPs 1, 3, 9, and 13 (24, 18, 1.9, and 1.3 nM, respectively). X-ray crystallography data obtained for MMP-3 cocrystallized with 20 gave detailed information on key binding interactions defining an overall scaffold geometry for piperazine-based MMP inhibitors.

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Road, Mason, Ohio 45040, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1 PRECURSOR	A, B	173	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
SPI	B	N-HYDROXY-1-(4-METHOXYPHENYL)SULFONYL-4-BENZYLOXYCARBONYL-PIPERAZINE-2-CARBOXAMIDE C20 H23 N3 O7 S DNGGPLKVDUPXFN-GOSISDBHSA-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 %)
SPI	IC50:  18   nM  BindingDB
SPI	IC50:  18   nM  Binding MOAD
SPI	IC50 :  18   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.294 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.27	α = 90
b = 78.54	β = 90
c = 106.58	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-22 
• Released Date: 2000-10-23 
Deposition Author(s): Cheng, M.Y., De, B., Pikul, S., Almstead, N.G., Natchus, M.G., Anastasio, M.V., McPhail, S.J., Snider, C.E., Taiwo, Y.O., Chen, L.Y.

Revision History 

• Version 1.0: 2000-10-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance