6KGL

LSD1-CoREST-S2101 N5 adduct model


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 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 --: --

  • DOI: 10.1002/cmdc.202000014
  • Primary Citation of Related Structures:  

  • 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 le ...

    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 submicromolar 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, Systems and Structural Biology Center, JAPAN.,RIKEN, Structural Biology Laboratory, JAPAN.,RIKEN, Yokoyama Laboratory, 1-7-22 Suehiro, Tsurumi, 230-0045, Yokohama, JAPAN.,RIKEN Center for Biosystems Dynamics Research, Laboratory for Epigenetics Drug Discovery, JAPAN.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1A
A
669Homo sapiensMutation(s): 0 
Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1)
EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens)
Go to Gene View: KDM1A
Go to UniProtKB:  O60341
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST corepressor 1
B
140Homo sapiensMutation(s): 0 
Gene Names: RCOR1 (KIAA0071, RCOR)
Find proteins for Q9UKL0 (Homo sapiens)
Go to Gene View: RCOR1
Go to UniProtKB:  Q9UKL0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DJ0
Query on DJ0

Download SDF File 
Download CCD File 
A
3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal
C16 H14 F2 O2
SMGWBKIRLMNBMH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 119.545α = 90.00
b = 178.549β = 90.00
c = 234.194γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release