4U43

MAP4K4 in complex with inhibitor (compound 6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fragment-based identification and optimization of a class of potent pyrrolo[2,1-f][1,2,4]triazine MAP4K4 inhibitors.

Wang, L.Stanley, M.Boggs, J.W.Crawford, T.D.Bravo, B.J.Giannetti, A.M.Harris, S.F.Magnuson, S.R.Nonomiya, J.Schmidt, S.Wu, P.Ye, W.Gould, S.E.Murray, L.J.Ndubaku, C.O.Chen, H.

(2014) Bioorg Med Chem Lett 24: 4546-4552

  • DOI: https://doi.org/10.1016/j.bmcl.2014.07.071
  • Primary Citation of Related Structures:  
    4U43, 4U44, 4U45

  • PubMed Abstract: 

    MAP4K4 has been shown to regulate key cellular processes that are tied to disease pathogenesis. In an effort to generate small molecule MAP4K4 inhibitors, a fragment-based screen was carried out and a pyrrolotriazine fragment with excellent ligand efficiency was identified. Further modification of this fragment guided by X-ray crystal structures and molecular modeling led to the discovery of a series of promising compounds with good structural diversity and physicochemical properties. These compounds exhibited single digit nanomolar potency and compounds 35 and 44 achieved good in vivo exposure.


  • Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: chen.huifen@gene.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 4
A, B
332Homo sapiensMutation(s): 0 
Gene Names: MAP4K4HGKKIAA0687NIK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O95819 (Homo sapiens)
Explore O95819 
Go to UniProtKB:  O95819
PHAROS:  O95819
GTEx:  ENSG00000071054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95819
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3D8
Query on 3D8

Download Ideal Coordinates CCD File 
C [auth A]N-(pyridin-3-yl)pyrrolo[2,1-f][1,2,4]triazin-4-amine
C11 H9 N5
KTWGHBNFKBORPM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3D8 BindingDB:  4U43 Kd: 4.80e+4 (nM) from 1 assay(s)
Binding MOAD:  4U43 Kd: 4.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.492α = 90
b = 80.643β = 90
c = 102.335γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Refinement description