7X9D

DNMT3B in complex with harmine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


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


Literature

Structural Insights into Inhibition of Human DNA Methyltransferases by Harmine

Cho, C.-C., Yuan, H.S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3BA, D286Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
PHAROS:  Q9UBC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBC3
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3-likeB, C204Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJW3 (Homo sapiens)
Explore Q9UJW3 
Go to UniProtKB:  Q9UJW3
PHAROS:  Q9UJW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJW3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HRM (Subject of Investigation/LOI)
Query on HRM
Download Ideal Coordinates CCD File 
E [auth A],
F [auth D]		7-METHOXY-1-METHYL-9H-BETA-CARBOLINE
C13 H12 N2 O
BXNJHAXVSOCGBA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.023α = 90
b = 236.161β = 90
c = 230.652γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data 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
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release