7SS1 | pdb_00007ss1

The structure of NTMT1 in complex with compound GD433

• PDB DOI: https://doi.org/10.2210/pdb7SS1/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-09 Released: 2022-11-16 
• Deposition Author(s): Yadav, R., Guangping, D., Deng, Y., Huang, R., Noinaj, N.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.299 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Discovery of a first-in-class small molecule inhibitor for Protein N-terminal methyltransferases 1/2

Yadav, R., Guangping, D., Deng, Y., Huang, R., Noinaj, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.22 kDa 
• Atom Count: 3,625 
• Modeled Residue Count: 441 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKF (Subject of Investigation/LOI)	D [auth A], F [auth B]	(1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluoro-3-hydroxyphenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate C20 H24 F N3 O3 S LRJXHGILPIXDQG-MRXNPFEDSA-N
SAH	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.299 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.909	α = 90
b = 89.909	β = 90
c = 141.542	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Yadav, R., Guangping, D., Deng, Y., Huang, R., Noinaj, N.

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

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary