4ZK5

MAP4K4 in complex with inhibitor GNE-495


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of GNE-495, a Potent and Selective MAP4K4 Inhibitor with Efficacy in Retinal Angiogenesis.

Ndubaku, C.O.Crawford, T.D.Chen, H.Boggs, J.W.Drobnick, J.Harris, S.F.Jesudason, R.McNamara, E.Nonomiya, J.Sambrone, A.Schmidt, S.Smyczek, T.Vitorino, P.Wang, L.Wu, P.Yeung, S.Chen, J.Chen, K.Ding, C.Z.Wang, T.Xu, Z.Gould, S.E.Murray, L.J.Ye, W.

(2015) Acs Med.Chem.Lett. 6: 913-918

  • DOI: 10.1021/acsmedchemlett.5b00174

  • PubMed Abstract: 
  • Diverse biological roles for mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) have necessitated the identification of potent inhibitors in order to study its function in various disease contexts. In particular, compounds that can be u ...

    Diverse biological roles for mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) have necessitated the identification of potent inhibitors in order to study its function in various disease contexts. In particular, compounds that can be used to carry out such studies in vivo would be critical for elucidating the potential for therapeutic intervention. A structure-based design effort coupled with property-guided optimization directed at minimizing the ability of the inhibitors to cross into the CNS led to an advanced compound 13 (GNE-495) that showed excellent potency and good PK and was used to demonstrate in vivo efficacy in a retinal angiogenesis model recapitulating effects that were observed in the inducible Map4k4 knockout mice.


    Organizational Affiliation

    Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.,Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
Find proteins for O95819 (Homo sapiens)
Go to Gene View: MAP4K4
Go to UniProtKB:  O95819
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
4P4
Query on 4P4

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Download CCD File 
A
8-amino-N-[1-(cyclopropylcarbonyl)azetidin-3-yl]-2-(3-fluorophenyl)-1,7-naphthyridine-5-carboxamide
GNE-495
C22 H20 F N5 O2
FYXCIBJXJYBWPX-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4P4IC50: 3.7 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.352α = 90.00
b = 89.335β = 90.00
c = 91.011γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Data collection