2Y6D | pdb_00002y6d

The Discovery of MMP7 Inhibitors Exploiting a Novel Selectivity Trigger

• PDB DOI: https://doi.org/10.2210/pdb2Y6D/pdb

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


• Deposited: 2011-01-20 Released: 2011-05-04 
• Deposition Author(s): Edman, K., Furber, M., Hemsley, P., Johansson, C., Pairaudeau, G., Petersen, J., Stocks, M., Tervo, A., Ward, A., Wells, E., Wissler, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The Discovery of Mmp7 Inhibitors Exploiting a Novel Selectivity Trigger.

Edman, K., Furber, M., Hemsley, P., Johansson, C., Pairaudeau, G., Petersen, J., Stocks, M., Tervo, A., Ward, A., Wells, E., Wissler, L.

(2011) ChemMedChem 6: 769

• PubMed: 21520417 
• DOI: https://doi.org/10.1002/cmdc.201000550
• Primary Citation of Related Structures:  
  2Y6C, 2Y6D

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Organizational Affiliation: 

Global Structural Chemistry, AstraZeneca Mölndal, Mölndal, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.13 kDa 
• Atom Count: 1,389 
• Modelled Residue Count: 160 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MATRILYSIN	A	174	Homo sapiens	Mutation(s): 0  EC: 3.4.24.23
UniProt & NIH Common Fund Data Resources
Find proteins for P09237 (Homo sapiens) Explore P09237  Go to UniProtKB:  P09237
PHAROS:  P09237 GTEx:  ENSG00000137673

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TQJ	H [auth A]	N-[(2S)-1-[4-(5-BROMOPYRIDIN-2-YL)PIPERAZIN-1-YL]SULFONYL-5-PYRIMIDIN-2-YL-PENTAN-2-YL]-N-HYDROXY-METHANAMIDE C19 H25 Br N6 O4 S KOKUKBSLFSEGAT-KRWDZBQOSA-N
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TQJ	BindingDB:  2Y6D	Ki: 79 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.59	α = 90
b = 76.59	β = 90
c = 60.924	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Edman, K., Furber, M., Hemsley, P., Johansson, C., Pairaudeau, G., Petersen, J., Stocks, M., Tervo, A., Ward, A., Wells, E., Wissler, L.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other