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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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:  

  • 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 inhibit ...

    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: 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
2QU
Query on 2QU

Download SDF File 
Download CCD File 
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 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 %)
2QUIC50: 17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.302α = 90.00
b = 88.688β = 90.00
c = 91.218γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTER-TNTrefinement
SCALAdata scaling
Blu-Icedata collection
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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