7EHZ | pdb_00007ehz

Structure of human NNMT in complex with macrocyclic peptide 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7EHZ

This is version 1.1 of the entry. See complete history

Literature

Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell.

Hayashi, K.Uehara, S.Yamamoto, S.Cary, D.R.Nishikawa, J.Ueda, T.Ozasa, H.Mihara, K.Yoshimura, N.Kawai, T.Ono, T.Yamamoto, S.Fumoto, M.Mikamiyama, H.

(2021) ACS Med Chem Lett 12: 1093-1101

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00134
  • Primary Citation Related Structures: 
    7EGU, 7EHZ, 7EI2

  • PubMed Abstract: 

    Nicotinamide N -methyltransferase (NNMT), which catalyzes the methylation of nicotinamide, is a cytosolic enzyme that has attracted much attention as a therapeutic target for a variety of diseases. However, despite the considerable interest in this target, reports of NNMT inhibitors have still been limited to date. In this work, utilizing in vitro translated macrocyclic peptide libraries, we identified peptide 1 as a novel class of NNMT inhibitors. Further exploration based on the X-ray cocrystal structures of the peptides with NNMT provided a dramatic improvement in inhibitory activity (peptide 23 : IC 50 = 0.15 nM). Furthermore, by balance of the peptides' lipophilicity and biological activity, inhibitory activity against NNMT in cell-based assay was successfully achieved (peptide 26 : cell-based IC 50 = 770 nM). These findings illuminate the potential of cyclic peptides as a relatively new drug discovery modality even for intracellular targets.


  • Organizational Affiliation
    • Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.

Macromolecule Content 

  • Total Structure Weight: 30.09 kDa 
  • Atom Count: 1,890 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 268 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferase259Homo sapiensMutation(s): 1 
Gene Names: NNMT
EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens)
Explore P40261 
Go to UniProtKB:  P40261
PHAROS:  P40261
GTEx:  ENSG00000166741 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40261
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
macrocyclic peptide 29synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
DI8
Query on DI8
B
L-PEPTIDE LINKINGC10 H11 N O2

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MEA
Query on MEA
B
L-PEPTIDE LINKINGC10 H13 N O2PHE
XA6
Query on XA6
B
L-PEPTIDE LINKINGC10 H12 N2 O3PHE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.081α = 90
b = 68.057β = 104.28
c = 45.205γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description