3P8H

Crystal structure of L3MBTL1 (MBT repeat) in complex with a nicotinamide antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small-molecule ligands of methyl-lysine binding proteins.

Herold, J.M.Wigle, T.J.Norris, J.L.Lam, R.Korboukh, V.K.Gao, C.Ingerman, L.A.Kireev, D.B.Senisterra, G.Vedadi, M.Tripathy, A.Brown, P.J.Arrowsmith, C.H.Jin, J.Janzen, W.P.Frye, S.V.

(2011) J.Med.Chem. 54: 2504-2511

  • DOI: 10.1021/jm200045v

  • PubMed Abstract: 
  • Proteins which bind methylated lysines ("readers" of the histone code) are important components in the epigenetic regulation of gene expression and can also modulate other proteins that contain methyl-lysine such as p53 and Rb. Recognition of methyl- ...

    Proteins which bind methylated lysines ("readers" of the histone code) are important components in the epigenetic regulation of gene expression and can also modulate other proteins that contain methyl-lysine such as p53 and Rb. Recognition of methyl-lysine marks by MBT domains leads to compaction of chromatin and a repressed transcriptional state. Antagonists of MBT domains would serve as probes to interrogate the functional role of these proteins and initiate the chemical biology of methyl-lysine readers as a target class. Small-molecule MBT antagonists were designed based on the structure of histone peptide-MBT complexes and their interaction with MBT domains determined using a chemiluminescent assay and ITC. The ligands discovered antagonize native histone peptide binding, exhibiting 5-fold stronger binding affinity to L3MBTL1 than its preferred histone peptide. The first cocrystal structure of a small molecule bound to L3MBTL1 was determined and provides new insights into binding requirements for further ligand design.


    Organizational Affiliation

    Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lethal(3)malignant brain tumor-like protein
A, B, C
323Homo sapiensMutation(s): 0 
Gene Names: L3MBTL1 (KIAA0681, L3MBT, L3MBTL)
Find proteins for Q9Y468 (Homo sapiens)
Go to Gene View: L3MBTL1
Go to UniProtKB:  Q9Y468
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
P8H
Query on P8H

Download SDF File 
Download CCD File 
A, B
3-bromo-5-[(4-pyrrolidin-1-ylpiperidin-1-yl)carbonyl]pyridine
C15 H20 Br N3 O
CQERVFFAOOUFEQ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P8HIC50: 4200 - 6000 nM (100) BINDINGDB
P8HKd: 5000 - 10000 nM (100) BINDINGDB
P8HKd: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 106.264α = 90.00
b = 106.264β = 90.00
c = 90.144γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
MxDCdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description