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: 39.75 kDa 
• Atom Count: 2831 
• Residue Count: 342 
• Unique protein chains: 1

1D8M

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR

• DOI: 10.2210/pdb1D8M/pdb

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


• Deposited: 1999-10-25 Released: 2000-10-25 
• Deposition Author(s): Pikul, S., Dunham, K.M., Almstead, N.G., De, B., Natchus, M.G., Taiwo, Y.O., Williams, L.E., Hynd, B.A., Hsieh, L.C., Janusz, M.J., Gu, F., Mieling, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.315 
• R-Value Work: 0.277 

Literature

Heterocycle-based MMP inhibitors with P2' substituents.

Pikul, S., Dunham, K.M., Almstead, N.G., De, B., Natchus, M.G., Taiwo, Y.O., Williams, L.E., Hynd, B.A., Hsieh, L.C., Janusz, M.J., Gu, F., Mieling, G.E.

(2001) Bioorg Med Chem Lett 11: 1009-1013

• PubMed: 11327577 
• DOI: 10.1016/s0960-894x(01)00137-8
• Primary Citation of Related Structures:  
  1G05, 1D8M


• PubMed Abstract: 
  

Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA. [e-mail]

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
BBH	B	1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO-HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE C19 H21 N3 O6 S SUSMVCKSLVPRCL-QGZVFWFLSA-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 %)
BBH	IC50 :  3.0999999046325684   nM  PDBBind
BBH	IC50:  3.0999999046325684   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.315 
• R-Value Work: 0.277 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.96	α = 90
b = 78.59	β = 90
c = 105.93	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: 1999-10-25 
• Released Date: 2000-10-25 
Deposition Author(s): Pikul, S., Dunham, K.M., Almstead, N.G., De, B., Natchus, M.G., Taiwo, Y.O., Williams, L.E., Hynd, B.A., Hsieh, L.C., Janusz, M.J., Gu, F., Mieling, G.E.

Revision History 

• Version 1.0: 2000-10-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance