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

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1038/nchembio.1157
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lethal(3)malignant brain tumor-like protein 3
A, B
332Homo sapiensMutation(s): 0 
Gene Names: KIAA1798L3MBTL3MBT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JM7 (Homo sapiens)
Explore Q96JM7 
Go to UniProtKB:  Q96JM7
GTEx:  ENSG00000198945 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JM7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UWN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C32 H43 N5 O2
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth A],
BA [auth A],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [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],
Z [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
UWN BindingDB:  4FL6 Kd: 120 (nM) from 1 assay(s)
IC50: min: 24, max: 64 (nM) from 3 assay(s)
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
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description