2OZR

MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid

• PDB DOI:  https://doi.org/10.2210/pdb2OZR/pdb

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


• Deposited: 2007-02-27 Released: 2007-07-24 
• Deposition Author(s): Johnson, A.R., Pavlovsky, A.G., Ortwine, D.F., Prior, F., Man, C.-F., Bornemeier, D.A., Banotai, C.A., Mueller, W.T., McConnell, P., Yan, C.H., Baragi, V., Lesch, C., Roark, W.H., Lie, J.J., Fasquelle, V., Wilson, M., Robertson, D., Datta, K., Guzman, R., Han, H.-K., Dyer, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.340 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 

Literature

Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects.

Johnson, A.R., Pavlovsky, A.G., Ortwine, D.F., Prior, F., Man, C.F., Bornemeier, D.A., Banotai, C.A., Mueller, W.T., McConnell, P., Yan, C., Baragi, V., Lesch, C., Roark, W.H., Wilson, M., Datta, K., Guzman, R., Han, H.K., Dyer, R.D.

(2007) J Biol Chem 282: 27781-27791

• PubMed: 17623656 
• DOI: https://doi.org/10.1074/jbc.M703286200
• Primary Citation of Related Structures:  
  2OW9, 2OZR


• PubMed Abstract: 
  

Matrix metalloproteinase-13 (MMP13) is a Zn(2+)-dependent protease that catalyzes the cleavage of type II collagen, the main structural protein in articular cartilage. Excess MMP13 activity causes cartilage degradation in osteoarthritis, making this protease an attractive therapeutic target. However, clinically tested MMP inhibitors have been associated with a painful, joint-stiffening musculoskeletal side effect that may be due to their lack of selectivity. In our efforts to develop a disease-modifying osteoarthritis drug, we have discovered MMP13 inhibitors that differ greatly from previous MMP inhibitors; they do not bind to the catalytic zinc ion, they are noncompetitive with respect to substrate binding, and they show extreme selectivity for inhibiting MMP13. By structure-based drug design, we generated an orally active MMP13 inhibitor that effectively reduces cartilage damage in vivo and does not induce joint fibroplasias in a rat model of musculoskeletal syndrome side effects. Thus, highly selective inhibition of MMP13 in patients may overcome the major safety and efficacy challenges that have limited previously tested non-selective MMP inhibitors. MMP13 inhibitors such as the ones described here will help further define the role of this protease in arthritis and other diseases and may soon lead to drugs that safely halt cartilage damage in patients.

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Organizational Affiliation: 

Department of Inflammation Molecular Sciences, Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 8-mer - A8 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 158.26 kDa 
• Atom Count: 11,898 
• Modelled Residue Count: 1,327 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B, C, D, E, F, G, H	170	Homo sapiens	Mutation(s): 0  Gene Names: MMP13 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452  Go to UniProtKB:  P45452
PHAROS:  P45452

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GG1	BB [auth G], GA [auth D], HB [auth H], N [auth A], NA [auth E], T [auth B], UA [auth F], Z [auth C]	4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID C26 H20 N2 O4 FLTYDFYSVZBKOB-UHFFFAOYSA-N
HAE	AA [auth C], HA [auth D], OA [auth E], VA [auth F]	ACETOHYDROXAMIC ACID C2 H5 N O2 RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN	BA [auth D], CA [auth D], CB [auth H], DB [auth H], I [auth A], IA [auth E], J [auth A], JA [auth E], O [auth B], P [auth B], PA [auth F], QA [auth F], U [auth C], V [auth C], WA [auth G], XA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	AB [auth G], DA [auth D], EA [auth D], EB [auth H], FA [auth D], FB [auth H], GB [auth H], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], Q [auth B], R [auth B], RA [auth F], S [auth B], SA [auth F], TA [auth F], W [auth C], X [auth C], Y [auth C], YA [auth G], ZA [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GG1	Binding MOAD:  2OZR	IC50: 0.67 (nM) from 1 assay(s)
	BindingDB:  2OZR	IC50: min: 0.67, max: 14 (nM) from 2 assay(s)
	PDBBind:  2OZR	IC50: 0.67 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.340 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.836	α = 90
b = 71.974	β = 124.59
c = 138.13	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Johnson, A.R., Pavlovsky, A.G., Ortwine, D.F., Prior, F., Man, C.-F., Bornemeier, D.A., Banotai, C.A., Mueller, W.T., McConnell, P., Yan, C.H., Baragi, V., Lesch, C., Roark, W.H., Lie, J.J., Fasquelle, V., Wilson, M., Robertson, D., Datta, K., Guzman, R., Han, H.-K., Dyer, R.D.

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2007-10-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description