2YIG

MMP13 in complex with a novel selective non zinc binding inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2YIG/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-05-13 Released: 2011-06-29 
• Deposition Author(s): Gerhardt, S., Hargreaves, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Selective Non Zinc Binding Inhibitors of Mmp13.

Savi, C.D., Morley, A.D., Ting, A., Nash, I., Karabelas, K., Wood, C.M., James, M., Norris, S.J., Karoutchi, G., Rankine, N., Hamlin, G., Macfaul, P.A., Ryan, D., Baker, S.V., Hargreaves, D., Gerhardt, S.

(2011) Bioorg Med Chem Lett 21: 4215

• PubMed: 21669521 
• DOI: https://doi.org/10.1016/j.bmcl.2011.05.075
• Primary Citation of Related Structures:  
  2YIG


• PubMed Abstract: 
  

  Directed screening has identified a novel series of MMP13 inhibitors that possess good levels of activity whilst possessing excellent selectivity over related MMPs. The binding mode of the series has been solved by co-crystallisation and demonstrates an interesting mode of inhibition without interaction with the catalytic zinc atom.

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Organizational Affiliation: 

AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

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)

Macromolecule Content

• Total Structure Weight: 39.87 kDa 
• Atom Count: 3,024 
• Modelled Residue Count: 333 
• 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  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
5EL	C [auth A], J [auth B]	4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO[2.2.2]OCT-3-YL]ETHYNYL}PHENOXY)-N-(PYRIDIN-4-YLMETHYL)BENZAMIDE C28 H27 N3 O3 FEOIBPWKGPFSTB-NDEPHWFRSA-N
ZN	D [auth A], F [auth A], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], G [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A], I [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5EL	BindingDB:  2YIG	IC50: min: 79, max: 125.89 (nM) from 3 assay(s)
	PDBBind:  2YIG	IC50: 79.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.417	α = 90
b = 36.074	β = 131.49
c = 95.206	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Gerhardt, S., Hargreaves, D.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Derived calculations
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other