6DTN | pdb_00006dtn

The structure of NTMT1 in complex with compound DC100-1

• PDB DOI: https://doi.org/10.2210/pdb6DTN/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-18 Released: 2019-04-03 
• Deposition Author(s): Noinaj, N., Chen, D., Huang, R.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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

• PubMed: 30883119 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00206
• Primary Citation Related Structures: 
  6DTN


• 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 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.

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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.
Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute of Inflammation, Immunology and Infectious Disease , Purdue University , West Lafayette , Indiana 47907 , United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 28.41 kDa 
• Atom Count: 2,174 
• Modeled Residue Count: 241 
• Deposited Residue Count: 249 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A [auth B]	241	Homo sapiens	Mutation(s): 0  Gene Names: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 EC: 2.1.1.244
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV86 (Homo sapiens) Explore Q9BV86  Go to UniProtKB:  Q9BV86
PHAROS:  Q9BV86 GTEx:  ENSG00000148335

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(6D6)PPKRIA(NH2), DC100-1	B [auth A]	8	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002319	B [auth A]	(6D6)PPKRIA(NH2), DC100-1	Oligopeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.166	α = 90
b = 73.166	β = 90
c = 82.361	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Noinaj, N., Chen, D., Huang, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1U01CA214649-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM117275-01A1

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
• Version 1.3: 2023-10-11
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary