6KGN

LSD1-CoREST-S2116 N5 adduct model


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.

Niwa, H.Sato, S.Handa, N.Sengoku, T.Umehara, T.Yokoyama, S.

(2020) ChemMedChem 15: 787-793

  • DOI: 10.1002/cmdc.202000014
  • Primary Citation of Related Structures:  
    6KGK, 6KGL, 6KGM, 6KGN, 6KGO, 6KGP, 6KGQ, 6KGR

  • PubMed Abstract: 
  • Lysine-specific demethylase 1 (LSD1) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the demethylation of histone H3 and regulates gene expression. Because it is implicated in the regulation of diseases such as acute myeloid leukemia, potent LSD1-specific inhibitors have been pursued ...

    Lysine-specific demethylase 1 (LSD1) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the demethylation of histone H3 and regulates gene expression. Because it is implicated in the regulation of diseases such as acute myeloid leukemia, potent LSD1-specific inhibitors have been pursued. Trans-2-phenylcyclopropylamine (2-PCPA)-based inhibitors featuring substitutions on the amino group have emerged, with sub-micromolar affinities toward LSD1 and high selectivities over monoamine oxidases (MAOs). We synthesized two N-alkylated 2-PCPA-based LSD1 inhibitors, S2116 and S2157, based on the previously developed S2101. S2116 and S2157 exhibited enhanced potency for LSD1 by 2.0- to 2.6-fold, as compared with S2101. In addition, they exhibited improved selectivity over MAOs. Structural analyses of LSD1 co-crystallized with S2101, S2116, S2157, or another N-alkylated inhibitor (FCPA-MPE) confirmed that the N-substituents enhance the potency of a 2-PCPA-based inhibitor of LSD1, without constituting the adduct formed with FAD.


    Organizational Affiliation

    RIKEN Yokoyama Laboratory, Yokohama, 230-0045, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1AA669Homo sapiensMutation(s): 0 
Gene Names: KDM1AAOF2KDM1KIAA0601LSD1
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens)
Explore O60341 
Go to UniProtKB:  O60341
PHAROS:  O60341
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60341
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
REST corepressor 1B140Homo sapiensMutation(s): 0 
Gene Names: RCOR1KIAA0071RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens)
Explore Q9UKL0 
Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKL0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
DJ0
Query on DJ0

Download Ideal Coordinates CCD File 
H [auth A]3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal
C16 H14 F2 O2
SMGWBKIRLMNBMH-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.451α = 90
b = 178.696β = 90
c = 235.256γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references