4L59

Crystal structure of the 3-MBT repeat domain of L3MBTL3 and UNC2533 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface.

Camerino, M.A.Zhong, N.Dong, A.Dickson, B.M.James, L.I.Baughman, B.M.Norris, J.L.Kireev, D.B.Janzen, W.P.Arrowsmith, C.H.Frye, S.V.

(2013) Medchemcomm 4: 1501-1507

  • DOI: 10.1039/C3MD00197K
  • Primary Citation of Related Structures:  
    4L59

  • PubMed Abstract: 
  • We recently reported the discovery of UNC1215, a potent and selective chemical probe for the L3MBTL3 methyllysine reader domain. In this article, we describe the development of structure-activity relationships (SAR) of a second series of potent L3MBT ...

    We recently reported the discovery of UNC1215, a potent and selective chemical probe for the L3MBTL3 methyllysine reader domain. In this article, we describe the development of structure-activity relationships (SAR) of a second series of potent L3MBTL3 antagonists which evolved from the structure of the chemical probe UNC1215. These compounds are selective for L3MBTL3 against a panel of methyllysine reader proteins, particularly the related MBT family proteins, L3MBTL1 and MBTD1. A co-crystal structure of L3MBTL3 and one of the most potent compounds suggests that the L3MBTL3 dimer rotates about the dimer interface to accommodate ligand binding.


    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. ; Tel: (919) 843-5486.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lethal(3)malignant brain tumor-like protein 3A317Homo sapiensMutation(s): 0 
Gene Names: L3MBTL3KIAA1798MBT1
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VZ
Query on 1VZ

Download CCD File 
A
4-(pyrrolidin-1-yl)-1-{4-[2-(pyrrolidin-1-yl)ethyl]phenyl}piperidine
C21 H33 N3
JPTZZWFKOIEDMU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.798α = 90
b = 104.798β = 90
c = 110.644γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2013-12-25
    Changes: Structure summary
  • Version 1.3: 2018-05-16
    Changes: Data collection, Database references