7XE2

Crystal structure of LSD2 in complex with trans-4-Br-PCPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

Niwa, H.Watanabe, C.Sato, S.Harada, T.Watanabe, H.Tabusa, R.Fukasawa, S.Shiobara, A.Hashimoto, T.Ohno, O.Nakamura, K.Tsuganezawa, K.Tanaka, A.Shirouzu, M.Honma, T.Matsuno, K.Umehara, T.

(2022) ACS Med Chem Lett 13: 1485-1492


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1B
A, B
793Homo sapiensMutation(s): 0 
Gene Names: KDM1BAOF1C6orf193LSD2
EC: 1.14.99.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB78 (Homo sapiens)
Explore Q8NB78 
Go to UniProtKB:  Q8NB78
PHAROS:  Q8NB78
GTEx:  ENSG00000165097 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NB78
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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F [auth A],
H [auth A],
S [auth B],
U [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
DIJ
Query on DIJ

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G [auth A],
I [auth A],
T [auth B],
V [auth B]
3-(4-bromophenyl)propanal
C9 H9 Br O
RXZJWVPNFPPSEM-UHFFFAOYSA-N
FLC
Query on FLC

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J [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PGE
Query on PGE

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K [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

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L [auth A],
M [auth A],
N [auth A],
O [auth A],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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C [auth A]
D [auth A]
E [auth A]
P [auth B]
Q [auth B]
C [auth A],
D [auth A],
E [auth A],
P [auth B],
Q [auth B],
R [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.582α = 90
b = 170.082β = 90
c = 201.107γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21K06461, 20H03388, 20K21406

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description