Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.37 kDa 
• Atom Count: 4817 
• Modelled Residue Count: 580 
• Deposited Residue Count: 664 
• Unique protein chains: 1

4ZK5

MAP4K4 in complex with inhibitor GNE-495

• PDB DOI: 10.2210/pdb4ZK5/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-04-29 Released: 2015-09-02 
• Deposition Author(s): Harris, S.F., Wu, P., Coons, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.265 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

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

• PubMed: 26288693 
• DOI: 10.1021/acsmedchemlett.5b00174
• Primary Citation of Related Structures:  
  4ZK5


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 4	A, B	332	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4P4	E [auth A]	8-amino-N-[1-(cyclopropylcarbonyl)azetidin-3-yl]-2-(3-fluorophenyl)-1,7-naphthyridine-5-carboxamide C22 H20 F N5 O2 FYXCIBJXJYBWPX-UHFFFAOYSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4P4	BindingDB:  4ZK5	IC50: 3.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.265 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.352	α = 90
b = 89.335	β = 90
c = 91.011	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-29 
• Released Date: 2015-09-02 
Deposition Author(s): Harris, S.F., Wu, P., Coons, M.

Revision History  

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