8PAW | pdb_00008paw

Crystal structure of MST1 with a MAP4K1 SMOL inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PAW

Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 72.89 kDa 
  • Atom Count: 4,844 
  • Modeled Residue Count: 557 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 4 37kDa subunit
A, B
312Homo sapiensMutation(s): 0 
Gene Names: STK4KRS2MST1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13043 (Homo sapiens)
Explore Q13043 
Go to UniProtKB:  Q13043
PHAROS:  Q13043
GTEx:  ENSG00000101109 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13043
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XQL
(Subject of Investigation/LOI)

Query on XQL



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
1-[3,5-bis(fluoranyl)-4-[[3-(1-propan-2-ylpyrazol-3-yl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-3-(2-methoxyethyl)urea
C23 H24 F2 N6 O3
AMSRRTXLQMAOQA-UHFFFAOYSA-N
CXS

Query on CXS



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
ASP

Query on ASP



Download:Ideal Coordinates CCD File
C [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.447α = 90
b = 105.627β = 90
c = 110.563γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-06-26 
  • Deposition Author(s): Friberg, A.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-01-29
    Changes: Database references