3LBZ

Crystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3LBZ

Classification: TRANSCRIPTION

Total Structure Weight: 31047.72

Macromolecule Entities
Molecule Chains Length Organism Details
B-cell lymphoma 6 protein A, B 127 Homo sapiens Fragment: BTB domain, residues 5-129
Mutation: C8Q, C67R, C84N
Gene Name(s): BCL6 Gene View BCL5 LAZ3 ZBTB27 ZNF51
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
Z89
Query on Z89

A, B (2R)-2-[(5Z)-5-(5-bromo-2-oxo-1,2-dihydro- 3H-indol-3-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin- 3-yl]butanedioic acid
N-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]- 5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE- 2-CARBOXAMIDE (Synonym)
C15 H9 Br N2 O6 S2
QGNRETMYLHRUBB-OZEWEUHLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Z88
Query on Z88

A, B N-[(4-bromophenyl)sulfonyl]acetamide
C8 H8 Br N O3 S
GUSSBUVTIMQOBB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
Z89 N/A in BindingDB
Ki: 147000 nM  BindingMOAD
Kd: 138000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.213
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 101.71 α = 90.00
b = 38.61 β = 114.70
c = 78.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-01-08
  • Released Date: 2010-04-28
  • Deposition author(s): Ghetu, A.F., Prive, G.G.

Revision History

  • Version 1_0: 2010-04-28

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance