6FZ3

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System.

Kersten, C.Fleischer, E.Kehrein, J.Borek, C.Jaenicke, E.Sotriffer, C.Brenk, R.

(2020) J Med Chem 63: 2095-2113

  • DOI: 10.1021/acs.jmedchem.9b00586
  • Primary Citation of Related Structures:  
    6EU5, 6EWF, 6F56, 6FZ2, 6FZ3, 6FZ5

  • PubMed Abstract: 
  • A model system of two related enzymes with conserved binding sites, namely N -myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified ...

    A model system of two related enzymes with conserved binding sites, namely N -myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified. For some ligands, a change in side-chain flexibility appears to be responsible for selective inhibition. Remarkably, this was observed for residues orienting their side chains away from the ligands. For other ligands, selectivity is caused by interfering with a water molecule that binds more strongly to the off-target than to the target. On the basis of this finding, a virtual screen for selective compounds was conducted, resulting in three hit compounds with the desired selectivity profile. This study delivers a guideline on how to assess selectivity-determining features in proteins with conserved binding sites and to translate this knowledge into the design of selective inhibitors.


    Organizational Affiliation

    Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020 Bergen, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1A, B403Homo sapiensMutation(s): 0 
Gene Names: NMT1NMT
EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens)
Explore P30419 
Go to UniProtKB:  P30419
PHAROS:  P30419
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30419
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
EBK (Subject of Investigation/LOI)
Query on EBK

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2,6-bis(chloranyl)-4-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide
C22 H26 Cl2 N6 O2 S
GQRWEJRYCBEXLY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EBK BindingDB:  6FZ3 Ki: min: 0.9, max: 40 (nM) from 4 assay(s)
IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.278α = 90
b = 58β = 92.18
c = 153.309γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany252061573

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2020-03-18
    Changes: Database references