8PAR

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

• PDB DOI: https://doi.org/10.2210/pdb8PAR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-06-08 Released: 2024-06-26 
• Deposition Author(s): Schaefer, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Starting Model: experimental

Literature

Identification and optimization of Azaindole based MAP4K1 Inhibitors and the discovery of BAY-405

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.03 kDa 
• Atom Count: 2,215 
• Modelled Residue Count: 268 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 1	A	308	Homo sapiens	Mutation(s): 2  Gene Names: MAP4K1, HPK1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XON (Subject of Investigation/LOI)	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	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 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.723	α = 90
b = 100.205	β = 90
c = 39.497	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release