4FL6

Crystal structure of the complex of the 3-MBT repeat domain of L3MBTL3 and UNC1215


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain.

James, L.I.Barsyte-Lovejoy, D.Zhong, N.Krichevsky, L.Korboukh, V.K.Herold, J.M.MacNevin, C.J.Norris, J.L.Sagum, C.A.Tempel, W.Marcon, E.Guo, H.Gao, C.Huang, X.P.Duan, S.Emili, A.Greenblatt, J.F.Kireev, D.B.Jin, J.Janzen, W.P.Brown, P.J.Bedford, M.T.Arrowsmith, C.H.Frye, S.V.

(2013) Nat Chem Biol 9: 184-191

  • DOI: 10.1038/nchembio.1157
  • Primary Citation of Related Structures:  
    4FL6

  • PubMed Abstract: 
  • We describe the discovery of UNC1215, a potent and selective chemical probe for the methyllysine (Kme) reading function of L3MBTL3, a member of the malignant brain tumor (MBT) family of chromatin-interacting transcriptional repressors. UNC1215 binds ...

    We describe the discovery of UNC1215, a potent and selective chemical probe for the methyllysine (Kme) reading function of L3MBTL3, a member of the malignant brain tumor (MBT) family of chromatin-interacting transcriptional repressors. UNC1215 binds L3MBTL3 with a K(d) of 120 nM, competitively displacing mono- or dimethyllysine-containing peptides, and is greater than 50-fold more potent toward L3MBTL3 than other members of the MBT family while also demonstrating selectivity against more than 200 other reader domains examined. X-ray crystallography identified a unique 2:2 polyvalent mode of interaction between UNC1215 and L3MBTL3. In cells, UNC1215 is nontoxic and directly binds L3MBTL3 via the Kme-binding pocket of the MBT domains. UNC1215 increases the cellular mobility of GFP-L3MBTL3 fusion proteins, and point mutants that disrupt the Kme-binding function of GFP-L3MBTL3 phenocopy the effects of UNC1215 on localization. Finally, UNC1215 was used to reveal a new Kme-dependent interaction of L3MBTL3 with BCLAF1, a protein implicated in DNA damage repair and apoptosis.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lethal(3)malignant brain tumor-like protein 3AB332Homo sapiensMutation(s): 0 
Gene Names: KIAA1798L3MBTL3MBT1
Find proteins for Q96JM7 (Homo sapiens)
Explore Q96JM7 
Go to UniProtKB:  Q96JM7
NIH Common Fund Data Resources
PHAROS  Q96JM7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UWN
Query on UWN

Download CCD File 
A
[2-(phenylamino)benzene-1,4-diyl]bis{[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone}
C32 H43 N5 O2
PQOOIERVZAXHBP-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UWNIC50:  64   nM  BindingDB
UWNKd:  120   nM  BindingDB
UWNIC50:  24   nM  BindingDB
UWNIC50:  49   nM  BindingDB
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.026α = 90
b = 54.372β = 97.11
c = 65.549γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references