Structure of PDB 6xmx Chain A Binding Site BS01

Receptor Information

>6xmx Chain A (length=122) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGL
FYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVM
ATAMYLQMEHVVDTCRKFIKAS

Ligand information

Ligand ID

U52

InChI

InChI=1S/C24H29ClN6O3/c1-14-7-15(2)12-31(11-14)24-27-10-18(25)22(29-24)28-17-5-6-19-16(8-17)9-20(23(33)30(19)4)34-13-21(32)26-3/h5-6,8-10,14-15H,7,11-13H2,1-4H3,(H,26,32)(H,27,28,29)/t14-,15+

InChIKey

GXTJETQFYHZHNB-GASCZTMLSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	CC1CC(CN(C1)c2ncc(c(n2)Nc3ccc4c(c3)C=C(C(=O)N4C)OCC(=O)NC)Cl)C
CACTVS 3.385	CNC(=O)COC1=Cc2cc(Nc3nc(ncc3Cl)N4C[CH](C)C[CH](C)C4)ccc2N(C)C1=O
OpenEye OEToolkits 2.0.6	C[C@@H]1C[C@@H](CN(C1)c2ncc(c(n2)Nc3ccc4c(c3)C=C(C(=O)N4C)OCC(=O)NC)Cl)C
CACTVS 3.385	CNC(=O)COC1=Cc2cc(Nc3nc(ncc3Cl)N4C[C@@H](C)C[C@@H](C)C4)ccc2N(C)C1=O

Formula

C24 H29 Cl N6 O3

Name

2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide

PDB chain

6xmx Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6xmx Small-molecule-induced polymerization triggers degradation of BCL6.
Resolution	3.7 Å
Binding residue (original residue number in PDB)	M51 A52 G55 Y58 Q113 E115 H116
Binding residue (residue number reindexed from 1)	M45 A46 G49 Y52 Q107 E109 H110
Annotation score	1

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:6xmx, PDBe:6xmx, PDBj:6xmx
PDBsum	6xmx
PubMed	33208943
UniProt	P41182\|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)

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