6WFK

Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Characterization of SpecificN-alpha-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.

Kung, P.P.Bingham, P.Burke, B.J.Chen, Q.Cheng, X.Deng, Y.L.Dou, D.Feng, J.Gallego, G.M.Gehring, M.R.Grant, S.K.Greasley, S.Harris, A.R.Maegley, K.A.Meier, J.Meng, X.Montano, J.L.Morgan, B.A.Naughton, B.S.Palde, P.B.Paul, T.A.Richardson, P.Sakata, S.Shaginian, A.Sonnenburg, W.K.Subramanyam, C.Timofeevski, S.Wan, J.Yan, W.Stewart, A.E.

(2020) ACS Med Chem Lett 11: 1175-1184

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00029
  • Primary Citation of Related Structures:  
    6WF3, 6WF5, 6WFG, 6WFK, 6WFN, 6WFO

  • PubMed Abstract: 

    Two novel compounds were identified as Naa50 binders/inhibitors using DNA-encoded technology screening. Biophysical and biochemical data as well as cocrystal structures were obtained for both compounds ( 3a and 4a ) to understand their mechanism of action. These data were also used to rationalize the binding affinity differences observed between the two compounds and a MLGP peptide-containing substrate. Cellular target engagement experiments further confirm the Naa50 binding of 4a and demonstrate its selectivity toward related enzymes (Naa10 and Naa60). Additional analogs of inhibitor 4a were also evaluated to study the binding mode observed in the cocrystal structures.


  • Organizational Affiliation

    Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 50
A, B, C
171Homo sapiensMutation(s): 0 
Gene Names: NAA50MAK3NAT13NAT5
EC: 2.3.1.258 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ1 (Homo sapiens)
Explore Q9GZZ1 
Go to UniProtKB:  Q9GZZ1
PHAROS:  Q9GZZ1
GTEx:  ENSG00000121579 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZZ1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
COA BindingDB:  6WFK Kd: 156 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.35α = 90
b = 102.38β = 106.92
c = 67.55γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description