5W5Q | pdb_00005w5q

MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl-3-(5-methyloxazol-2-yl)but-1-yn-1-yl)-6,7-dihydro-5H-5,7-methanobenzo[c]imidazo[1,2-a]azepine-2,3-dicarboxamide)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.235 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.209 (Depositor) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5W5Q

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1).

Feng, J.A., Lee, P., Alaoui, M.H., Barrett, K., Castanedo, G., Godemann, R., McEwan, P., Wang, X., Wu, P., Zhang, Y., Harris, S.F., Staben, S.T.

(2019) ACS Med Chem Lett 10: 1260-1265

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00658
  • Primary Citation Related Structures: 
    5W5Q, 6MYN

  • PubMed Abstract: 

    We previously disclosed a series of type I 1/2 inhibitors of NF-κB inducing kinase (NIK). Inhibition of NIK by these compounds was found to be strongly dependent on the inclusion and absolute stereochemistry of a propargyl tertiary alcohol as it forms critical hydrogen bonds (H-bonds) with NIK. We report that inhibition of protein kinase D1 (PKD1) by this class of compounds is not dependent on H-bond interactions of this tertiary alcohol. This feature was leveraged in the design of highly selective inhibitors of PKD1 that no longer inhibit NIK. A structure-based hypothesis based on the position and flexibility of the α-C-helix of PKD1 vs NIK is presented.

    • Organizational Affiliation: 
    • Genentech, 1 DNA way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 76.18 kDa 
  • Atom Count: 5,013 
  • Modeled Residue Count: 588 
  • 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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9X4
(Subject of Investigation/LOI)

Query on 9X4


Download:Ideal Coordinates CCD File
C [auth A](5s,7s)-N~3~-methyl-10-[3-methyl-3-(5-methyl-1,3-oxazol-2-yl)but-1-yn-1-yl]-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide
C25 H25 N5 O3
BVQAJAHFWBYNPF-IYBDPMFKSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.209 (Depositor) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.611α = 90
b = 89.676β = 90
c = 90.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-13
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references