7OKL: Human BCL6 BTB domain

Crystal structure of human BCL6 BTB domain in complex with compound 13e. Determined by X-ray diffraction at 1.2 Å resolution. Released 8 Dec 2021.

Method: X-ray diffraction
Resolution: 1.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,529
Mol. weight: 16.18 kDa
Ligands: VJ5
Released: 8 Dec 2021

Explore 7OKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OKL contains 8 α-helices and 5 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
α-helix	14-27	14
β-strand	34-38	5	2
β-strand	41-45	5	2
α-helix	47-53	7
α-helix	55-61	7
α-helix	66-68	3
β-strand	71-73	3	2
α-helix	74-75	2
α-helix	80-92	13
α-helix	102-112	11
α-helix	115-128	14

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-cell lymphoma 6 protein	A	protein	128	Homo sapiens	P41182 (AlphaFold model)
Ala-trp-val-ile-pro-ala	B	protein	6	synthetic construct

Sequence of entity 1 (A), FASTA

>7OKL_1 B-cell lymphoma 6 protein (chains A)
GPGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIF
TDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTC
RKFIKASE

Sequence of entity 2 (B), FASTA

>7OKL_2 ALA-TRP-VAL-ILE-PRO-ALA (chains B)
AWVIPA

Ligands and cofactors

ID	Name	Formula	Copies
VJ5	2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-[[(1R)-1-pyrimidin-2-ylethyl]amino]q…	C22 H18 Cl N7 O	1

Water and common crystallization additives (EDO, CL, DMS) are not listed.

Primary citation

Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket. Lloyd, M.G., Huckvale, R., Cheung, K.J. et al. J Med Chem (2021) 64:17079-17097. DOI 10.1021/acs.jmedchem.1c00946 · PubMed

Other PDB entries of the same protein (UniProt P41182 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LWE 1.17 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-7629
7RV1 1.17 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8826
7LWF 1.22 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-9320
7RV4 1.25 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-9153
7RV8 1.25 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-10268
7RUY 1.27 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8388
7RV2 1.29 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8828
1R29 1.3 Å, Crystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1.3 Angstrom
7LWG 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-12694
7RUW 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-7859
7RUX 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8311
7OKG 1.32 Å, Crystal structure of human BCL6 BTB domain in complex with compound 8e

Browse structure collections

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