7KPU

Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue with a C-3 linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D.

Deng, Y.Deng, S.Ho, Y.H.Gardner, S.M.Huang, Z.Marmorstein, R.Huang, R.

(2021) J Med Chem 64: 8263-8271

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00141
  • Primary Citation of Related Structures:  
    7KD7, 7KPU

  • PubMed Abstract: 

    Protein N-terminal acetyltransferase D (NatD, NAA40) that specifically acetylates the alpha-N-terminus of histone H4 and H2A has been implicated in various diseases, but no inhibitor has been reported for this important enzyme. Based on the acetyl transfer mechanism of NatD, we designed and prepared a series of highly potent NatD bisubstrate inhibitors by covalently linking coenzyme A to different peptide substrates via an acetyl or propionyl spacer. The most potent bisubstrate inhibitor displayed an apparent K i value of 1.0 nM. Biochemical studies indicated that bisubstrate inhibitors are competitive to the peptide substrate and noncompetitive to the cofactor, suggesting that NatD undergoes an ordered Bi-Bi mechanism. We also demonstrated that these inhibitors are highly specific toward NatD, displaying about 1000-fold selectivity over other closely related acetyltransferases. High-resolution crystal structures of NatD bound to two of these inhibitors revealed the molecular basis for their selectivity and inhibition mechanism, providing a rational path for future inhibitor development.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 40A [auth D],
C [auth A]
204Homo sapiensMutation(s): 0 
Gene Names: NAA40NAT11PATT1
EC: 2.3.1.257
UniProt & NIH Common Fund Data Resources
Find proteins for Q86UY6 (Homo sapiens)
Explore Q86UY6 
Go to UniProtKB:  Q86UY6
PHAROS:  Q86UY6
GTEx:  ENSG00000110583 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86UY6
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bisubstrate analogue (CMC-ACE-SER-GLY-ARG-GLY-LYS)B [auth E],
D [auth B]
5Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WZG (Subject of Investigation/LOI)
Query on WZG

Download Ideal Coordinates CCD File 
H [auth E],
Q [auth B]
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-[(3-{[2-(methylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-4-oxobutyl dihydrogen diphosphate (non-preferred name)
C22 H38 N7 O16 P3 S
NYNSZKVCAZNSEH-GORZOVPNSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
G [auth D]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth D],
F [auth D],
K [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
O [auth A],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACE (Subject of Investigation/LOI)
Query on ACE

Download Ideal Coordinates CCD File 
J [auth E],
S [auth B]
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
NH2
Query on NH2

Download Ideal Coordinates CCD File 
I [auth E],
R [auth B]
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.317α = 90
b = 74.164β = 90
c = 127.022γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description