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 4U45 | pdb_00004u45

MAP4K4 in complex with inhibitor (compound 25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 
    0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4U45

Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 76.26 kDa 
  • Atom Count: 4,960 
  • Modeled Residue Count: 584 
  • Deposited Residue Count: 664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 4
A, B
332Homo sapiensMutation(s): 0 
Gene Names: MAP4K4, HGK, KIAA0687, NIK
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free:  0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.915α = 90
b = 89.018β = 90
c = 91.396γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy