7B7R

MEK1 in complex with compound 4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Literature

Fragment-Based Discovery of Novel Allosteric MEK1 Binders.

Di Fruscia, P., Edfeldt, F., Shamovsky, I., Collie, G.W., Aagaard, A., Barlind, L., Borjesson, U., Hansson, E.L., Lewis, R.J., Nilsson, M.K., Oster, L., Pemberton, J., Ripa, L., Storer, R.I., Kack, H.

(2021) ACS Med Chem Lett 12: 302-308

  • DOI: 10.1021/acsmedchemlett.0c00563
  • Primary Citation of Related Structures:  
    7B3M, 7B7R, 7B94, 7B9L

  • PubMed Abstract: 

    • The MEK1 kinase plays a critical role in key cellular processes, and as such, its dysfunction is strongly linked to several human diseases, particularly cancer. MEK1 has consequently received considerable attention as a drug target, and a significant number of small-molecule inhibitors of this kinase have been reported ...

    The MEK1 kinase plays a critical role in key cellular processes, and as such, its dysfunction is strongly linked to several human diseases, particularly cancer. MEK1 has consequently received considerable attention as a drug target, and a significant number of small-molecule inhibitors of this kinase have been reported. The majority of these inhibitors target an allosteric pocket proximal to the ATP binding site which has proven to be highly druggable, with four allosteric MEK1 inhibitors approved to date. Despite the significant attention that the MEK1 allosteric site has received, chemotypes which have been shown structurally to bind to this site are limited. With the aim of discovering novel allosteric MEK1 inhibitors using a fragment-based approach, we report here a screening method which resulted in the discovery of multiple allosteric MEK1 binders, one series of which was optimized to sub-μM affinity for MEK1 with promising physicochemical and ADMET properties.

    Organizational Affiliation: 

    Structure Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1,Dual specificity mitogen-activated protein kinase kinase 1A, B326Homo sapiensMutation(s): 0 
Gene Names: MAP2K1, MEK1, PRKMK1
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
T1K (Subject of Investigation/LOI)
Query on T1K
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		2-[5-[ethyl(methyl)amino]imidazo[1,2-a]pyrimidin-7-yl]phenol
C15 H16 N4 O
SYAAVLGXDXOBNI-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
K [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 71.65β = 90
c = 157.81γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2020-12-11 
  • Released Date: 2021-03-03 
    • Deposition Author(s): Kack, H., Oster, L.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release