7T0U

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

PDB DOI: https://doi.org/10.2210/pdb7T0U/pdb

Classification: TRANSCRIPTION/TRANSCRIPTION INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-11-30 Released: 2022-11-09
Deposition Author(s): Kuntz, D.A., Prive, G.G.
Funding Organization(s): Ontario Institute for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.180
R-Value Work: 0.141
R-Value Observed: 0.142

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

Kuntz, D.A., Prive, G.G.

To be published.

Macromolecule Content

Total Structure Weight: 61.64 kDa
Atom Count: 4,633
Modelled Residue Count: 490
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of B-cell lymphoma 6 protein	A, B, C, D	127	Homo sapiens	Mutation(s): 3 Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182 Go to UniProtKB: P41182
PHAROS: P41182 GTEx: ENSG00000113916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E3I (Subject of Investigation/LOI) Query on E3I Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	H [auth A], I [auth B], L [auth C], M [auth D]	3-chloro-5-{7-[2-({5-chloro-2-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-2-(trifluoromethyl)-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide C₃₀ H₂₉ Cl₂ F₃ N₈ O₅ KEVLSWXLPHCNJR-AWEZNQCLSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth D]	E [auth A], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain O [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D]	G [auth A], J [auth B], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain P [auth D]