4WMR

STRUCTURE OF MCL1 BOUND TO BRD inhibitor ligand 1 AT 1.7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report



Literature

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

Clifton, M.C.Dranow, D.M.Leed, A.Fulroth, B.Fairman, J.W.Abendroth, J.Atkins, K.A.Wallace, E.Fan, D.Xu, G.Ni, Z.J.Daniels, D.Van Drie, J.Wei, G.Burgin, A.B.Golub, T.R.Hubbard, B.K.Serrano-Wu, M.H.

(2015) PLoS One 10: e0125010-e0125010

  • DOI: 10.1371/journal.pone.0125010
  • Primary Citation of Related Structures:  
    4WMR, 4WMS, 4WMT, 4WMU, 4WMV, 4WMW, 4WMX

  • PubMed Abstract: 
  • Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advan ...

    Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.


    Organizational Affiliation

    The Broad Institute, Cambridge, Massachusetts, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A150Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS  Q07820
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
865
Query on 865

Download CCD File 
A
7-[2-(1H-imidazol-1-yl)-4-methylpyridin-3-yl]-3-[3-(naphthalen-1-yloxy)propyl]-1-[2-oxo-2-(piperazin-1-yl)ethyl]-1H-indole-2-carboxylic acid
C37 H36 N6 O4
ZZKICOFWGKKSRR-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.77α = 90
b = 38.41β = 102.6
c = 48.33γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release