8ULZ | pdb_00008ulz

LSD1-CoREST in complex with T18 and SNAG peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 
    0.231 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1

Caroli, J., Mattevi, A.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein SNAI1A [auth C]9Homo sapiensMutation(s): 0 
Gene Names: SNAI1, SNAH
UniProt & NIH Common Fund Data Resources
Find proteins for O95863 (Homo sapiens)
Explore O95863 
Go to UniProtKB:  O95863
PHAROS:  O95863
GTEx:  ENSG00000124216 
Entity Groups  
UniProt GroupO95863
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1AB [auth A]871Homo sapiensMutation(s): 0 
Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1
EC: 1.14.99.66
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens)
Explore O60341 
Go to UniProtKB:  O60341
PHAROS:  O60341
GTEx:  ENSG00000004487 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60341
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REST corepressor 1C [auth B]144Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKL0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YAO (Subject of Investigation/LOI)
Query on YAO
Download Ideal Coordinates CCD File 
D [auth A][(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)
C43 H48 N10 O17 P2
TVSQFEAYGQYMKN-MSBGJGFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free:  0.231 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.371α = 90
b = 177.771β = 90
c = 234.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG19808

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release