8JF5 | pdb_00008jf5

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440

• PDB DOI: https://doi.org/10.2210/pdb8JF5/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-17 Released: 2024-05-22 
• Deposition Author(s): Fukushima, H., Machida, T., Yamashita, S., Suzuki, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

TAS1440, a histone H3 competitive LSD1 inhibitor, activates both TGF-beta and notch signaling pathways via INSM1 dissociation in neuroendocrine small cell lung cancer

Machida, T., Tsukioka, S., Gong, Y., Onodera, A., Nakayama, A., Hashimoto, N., Ohkubo, S., Tanaka, T.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 90.66 kDa 
• Atom Count: 5,956 
• Modeled Residue Count: 794 
• Deposited Residue Count: 798 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	663	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1.14.99.66 (PDB Primary Data), 1.14.11 (UniProt), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	B	135	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UEU (Subject of Investigation/LOI)	F [auth A]	4-[5-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-2-[2-fluoranyl-4-(2-methyl-2-oxidanyl-propyl)phenyl]phenyl]-2-fluoranyl-benzenecarbonitrile C28 H27 F2 N3 O2 SADVGAWKLORBLA-OAQYLSRUSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.772	α = 90
b = 179.115	β = 90
c = 235.029	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Fukushima, H., Machida, T., Yamashita, S., Suzuki, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release