4JPA

Mmp13 in complex with a piperazine hydantoin ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hydantoin based inhibitors of MMP13--discovery of AZD6605.

De Savi, C.Waterson, D.Pape, A.Lamont, S.Hadley, E.Mills, M.Page, K.M.Bowyer, J.Maciewicz, R.A.

(2013) Bioorg.Med.Chem.Lett. 23: 4705-4712

  • DOI: 10.1016/j.bmcl.2013.05.089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Piperidine ether and aryl piperazine hydantoins are reported as potent inhibitors of MMP13. A medicinal chemistry campaign focused on replacing the reverse hydroxamate zinc binding group associated with historical inhibitors with a hydantoin zinc bin ...

    Piperidine ether and aryl piperazine hydantoins are reported as potent inhibitors of MMP13. A medicinal chemistry campaign focused on replacing the reverse hydroxamate zinc binding group associated with historical inhibitors with a hydantoin zinc binding group then optimising MMP13 potency, solubility and DMPK properties whilst maintaining good selectivity over MMP14. A number of high quality candidates were progressed and following rat and dog safety evaluation, AZD6605 (3m) was identified as a candidate drug.


    Organizational Affiliation

    Oncology Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. chris.desavi2@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
173Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AZ6
Query on AZ6

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Download CCD File 
A, B
3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile
C21 H23 N7 O5 S
PKCWEIUDUFDFAG-OAQYLSRUSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZ6IC50: 3.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.771α = 90.00
b = 35.986β = 134.99
c = 101.492γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
StructureStudiodata collection
AMoREphasing
d*TREKdata scaling
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description