8PAR | pdb_00008par

Crystal structure of human MAP4K1 with an inhibitor, BAY-405


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.292 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of BAY-405: An Azaindole-Based MAP4K1 Inhibitor for the Enhancement of T-Cell Immunity against Cancer.

Mowat, J.Carretero, R.Leder, G.Aiguabella Font, N.Neuhaus, R.Berndt, S.Gunther, J.Friberg, A.Schafer, M.Briem, H.Raschke, M.Miyatake Ondozabal, H.Buchmann, B.Boemer, U.Kreft, B.Hartung, I.V.Offringa, R.

(2024) J Med Chem 67: 17429-17453

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01325
  • Primary Citation of Related Structures:  
    8PAR, 8PAS, 8PAU, 8PAV, 8PAW

  • PubMed Abstract: 

    Mitogen-activated protein kinase kinase kinase kinase 1 (MAP4K1) is a serine/threonine kinase that acts as an immune checkpoint downstream of T-cell receptor stimulation. MAP4K1 activity is enhanced by prostaglandin E2 (PGE2) and transforming growth factor beta (TGFβ), immune modulators commonly present in the tumor microenvironment. Therefore, its pharmacological inhibition is an attractive immuno-oncology concept for inducing therapeutic T-cell responses in cancer patients. Here, we describe the systematic optimization of azaindole-based lead compound 1 , resulting in the discovery of potent and selective MAP4K1 inhibitor 38 (BAY-405) that displays nanomolar potency in biochemical and cellular assays as well as in vivo exposure after oral dosing. BAY-405 enhances T-cell immunity and overcomes the suppressive effect of PGE2 and TGFβ. Treatment of tumor-bearing mice shows T-cell-dependent antitumor efficacy. MAP4K1 inhibition in conjunction with PD-L1 blockade results in a superior antitumor impact, illustrating the complementarity of the single agent treatments.


  • Organizational Affiliation
    • Bayer AG, Pharmaceutical R&D, 13342 Berlin, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 1308Homo sapiensMutation(s): 2 
Gene Names: MAP4K1HPK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens)
Explore Q92918 
Go to UniProtKB:  Q92918
PHAROS:  Q92918
GTEx:  ENSG00000104814 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92918
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XON (Subject of Investigation/LOI)
Query on XON

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[3,5-bis(fluoranyl)-4-[[3-[1-(trifluoromethyl)cyclopropyl]-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-2,9-dioxa-4-azaspiro[5.5]undec-3-en-3-amine
C25 H23 F5 N4 O3
FXMIIWBGTCDJJQ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.292 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.723α = 90
b = 100.205β = 90
c = 39.497γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-26 
  • Deposition Author(s): Schaefer, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references, Structure summary