Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40025.90 
• Atom Count: 2778 
• Residue Count: 346 
• Unique protein chains: 1

1D7X

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A MODIFIED PROLINE SCAFFOLD BASED INHIBITOR.

• DOI: 10.2210/pdb1D7X/pdb

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


• Deposited: 1999-10-20 Released: 2000-10-23 
• Deposition Author(s): Cheng, M.Y., Natchus, M.G., De, B., Almstead, N.G., Pikul, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.227 
• R-Value Work: 0.262 

Literature

Design, synthesis, and biological evaluation of matrix metalloproteinase inhibitors derived from a modified proline scaffold.

Cheng, M., De, B., Almstead, N.G., Pikul, S., Dowty, M.E., Dietsch, C.R., Dunaway, C.M., Gu, F., Hsieh, L.C., Janusz, M.J., Taiwo, Y.O., Natchus, M.G., Hudlicky, T., Mandel, M.

(1999) J.Med.Chem. 42: 5426-5436

• PubMed: 10639284 


• PubMed Abstract: 
  

The synthesis and structure-activity relationship (SAR) studies of a series of proline-based matrix metalloproteinase inhibitors are described. The data reveal a remarkable potency enhancement in those compounds that contain an sp(2) center at the C-4 carbon of the ring relative to similar, saturated compounds. This effect was noted in compounds that contained a functionalized oxime moiety or an exomethylene at C-4, and the potencies were typically <10 nM for MMP-3 and <100 nM for MMP-1. Comparisons were then made against compounds with similar functionality where the C-4 carbon was reduced to sp(3) hybridization and the effect was typically an order of magnitude loss in potency. A comparison of compounds 14 and 34 exemplifies this observation. An X-ray structure was obtained for a stromelysin-inhibitor complex which provided insights into the SAR and selectivity trends observed within the series. In vitro intestinal permeability data for many compounds was also accumulated.

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Organizational Affiliation: 

Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: MMP3 Go to UniProtKB:  P08254

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SPC	A, B	N-HYDROXY 1N(4-METHOXYPHENYL)SULFONYL-4-(Z,E-N-METHOXYIMINO)PYRROLIDINE-2R-CARBOXAMIDE C13 H19 N3 O6 S OJLWCTMBGWSVFC-JOYOIKCWSA-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 %)
SPC	IC50: 19 nM (100) BINDINGDB
SPC	IC50: 3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.227 
• R-Value Work: 0.262 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 37.850	α = 90.00
b = 78.220	β = 90.00
c = 104.740	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
SMART	data reduction
X-PLOR	refinement
X-PLOR	model building
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-20 
• Released Date: 2000-10-23 
• Deposition Author(s): Cheng, M.Y., Natchus, M.G., De, B., Almstead, N.G., Pikul, S.

Revision History 

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