4OBP

MAP4K4 in complex with inhibitor (compound 29), 6-(2-FLUOROPYRIDIN-4-YL)PYRIDO[3,2-D]PYRIMIDIN-4-AMINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Literature

Discovery of Selective 4-Amino-pyridopyrimidine Inhibitors of MAP4K4 Using Fragment-Based Lead Identification and Optimization.

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

(2014) J Med Chem 57: 3484-3493

  • DOI: 10.1021/jm500155b
  • Primary Citation of Related Structures:  
    4OBO, 4OBP, 4OBQ

  • PubMed Abstract: 

    • Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is a serine/threonine kinase implicated in the regulation of many biological processes. A fragment-based lead discovery approach was used to generate potent and selective MAP4K4 inhibitors. The fragment hit pursued in this article had excellent ligand efficiency (LE), an important attribute for subsequent successful optimization into drug-like lead compounds ...

    Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is a serine/threonine kinase implicated in the regulation of many biological processes. A fragment-based lead discovery approach was used to generate potent and selective MAP4K4 inhibitors. The fragment hit pursued in this article had excellent ligand efficiency (LE), an important attribute for subsequent successful optimization into drug-like lead compounds. The optimization efforts eventually led us to focus on the pyridopyrimidine series, from which 6-(2-fluoropyridin-4-yl)pyrido[3,2-d]pyrimidin-4-amine (29) was identified. This compound had low nanomolar potency, excellent kinase selectivity, and good in vivo exposure, and demonstrated in vivo pharmacodynamic effects in a human tumor xenograft model.

    Organizational Affiliation: 

    Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 4A, B332Homo sapiensMutation(s): 0 
Gene Names: HGK, KIAA0687, MAP4K4, 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2QU
Query on 2QU
Download Ideal Coordinates CCD File 
E [auth A]6-(2-fluoropyridin-4-yl)pyrido[3,2-d]pyrimidin-4-amine
C12 H8 F N5
CLODUYRNZMIONW-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2QU BindingDB:  4OBP IC50: min: 11.5, max: 200 (nM) from 7 assay(s)
Binding MOAD:  4OBP IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.302α = 90
b = 88.688β = 90
c = 91.218γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2014-01-07 
  • Released Date: 2014-04-23 
    • Deposition Author(s): Harris, S.F., Wu, P.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description