3I7G | pdb_00003i7g

MMP-13 in complex with a non zinc-chelating inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3I7G/pdb

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


• Deposited: 2009-07-08 Released: 2009-09-01 
• Deposition Author(s): Farrow, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.228 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors.

Heim-Riether, A., Taylor, S.J., Liang, S., Gao, D.A., Xiong, Z., Michael August, E., Collins, B.K., Farmer, B.T., Haverty, K., Hill-Drzewi, M., Junker, H.D., Mariana Margarit, S., Moss, N., Neumann, T., Proudfoot, J.R., Keenan, L.S., Sekul, R., Zhang, Q., Li, J., Farrow, N.A.

(2009) Bioorg Med Chem Lett 19: 5321-5324

• PubMed: 19692239 
• DOI: https://doi.org/10.1016/j.bmcl.2009.07.151
• Primary Citation Related Structures: 
  3I7G, 3I7I


• PubMed Abstract: 
  

  Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1' pocket.

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Organizational Affiliation: 
• Boehringer Ingelheim Pharmaceuticals, Department of Medicinal Chemistry, 900 Ridgebury Rd, Ridgefield, CT 06877, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.44 kDa 
• Atom Count: 3,006 
• Modeled Residue Count: 328 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	171	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 GTEx:  ENSG00000137745

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
732	I [auth A]	5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide C20 H23 Cl N2 O3 SOSADZXKACRLDA-SFHVURJKSA-N
ZN	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	H [auth A], O [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.228 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.77	α = 90
b = 36.1	β = 130.77
c = 95.333	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Farrow, N.A.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations