6DTN

The structure of NTMT1 in complex with compound DC100-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of Bisubstrate Inhibitors for Protein N-Terminal Methyltransferase 1.

Chen, D.Dong, G.Noinaj, N.Huang, R.

(2019) J Med Chem 62: 3773-3779

  • DOI: 10.1021/acs.jmedchem.9b00206
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein N-terminal methyltransferase 1 (NTMT1) plays an important role in regulating mitosis and DNA repair. Here, we describe the discovery of a potent NTMT1 bisubstrate inhibitor 4 (IC 50 = 35 ± 2 nM) that exhibits greater than 100-fold ...

    Protein N-terminal methyltransferase 1 (NTMT1) plays an important role in regulating mitosis and DNA repair. Here, we describe the discovery of a potent NTMT1 bisubstrate inhibitor 4 (IC 50 = 35 ± 2 nM) that exhibits greater than 100-fold selectivity against a panel of methyltransferases. We also report the first crystal structure of NTMT1 in complex with an inhibitor, which revealed that 4 occupies substrate and cofactor binding sites of NTMT1.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal Xaa-Pro-Lys N-methyltransferase 1
B
241Homo sapiensMutation(s): 0 
Gene Names: NTMT1C9orf32METTL11ANRMTNRMT1AD-003
EC: 2.1.1.244
Find proteins for Q9BV86 (Homo sapiens)
Go to UniProtKB:  Q9BV86
NIH Common Fund Data Resources
PHAROS  Q9BV86
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
(6D6)PPKRIA(NH2), DC100-1
A
8synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002319
Query on PRD_002319
A(6D6)PPKRIA(NH2), DC100-1Oligopeptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.166α = 90
b = 73.166β = 90
c = 82.361γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1U01CA214649-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM117275-01A1

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence