6K3E

LSD1/Co-Rest structure with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

LSD1/Co-Rest structure with an inhibitor

Jiang, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1AA662Homo 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
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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 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D3U (Subject of Investigation/LOI)
Query on D3U

Download Ideal Coordinates CCD File 
M [auth A]2-PCPA derivative
C36 H41 N9 O15 P2
LTYXJNFFNLDHFB-VXYXFEBYSA-N
 Ligand Interaction
CW0
Query on CW0

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C [auth A]piperidin-4-ylmethyl 4-fluoranyl-4-[[[(1~{R},2~{S})-2-phenylcyclopropyl]amino]methyl]piperidine-1-carboxylate
C22 H32 F N3 O2
CMYNDDNZDLGSJZ-VQTJNVASSA-N
 Ligand Interaction
CVO
Query on CVO

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EA [auth A]piperidin-4-ylmethyl 4-(aminomethyl)-4-fluoranyl-piperidine-1-carboxylate
C13 H24 F N3 O2
DOWIQGRBTWGHLC-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

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D [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
PEG
Query on PEG

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AA [auth A],
BA [auth A],
Z [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

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F [auth A],
G [auth A],
H [auth A]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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E [auth A],
FA [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth A],
DA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.51α = 90
b = 179.44β = 90
c = 234.41γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-05-20 
  • Deposition Author(s): Wang, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81620108027

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release