SMTL ID : 7qk0.1

Crystal structure of human BCL6 BTB domain in complex with compound 12a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x EBL: (2~{S})-10-[[5-chloranyl-2-[(3~{S},5~{R})-3-methyl-5-oxidanyl-piperidin-1-yl]pyrimidin-4-yl]amino]-2-cyclopropyl-3,3-bis(fluoranyl)-7-methyl-2,4-dihydro-1~{H}-[1,4]oxazepino[2,3-c]quinolin-6-one(Non-covalent)

EBL.1: 18 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, F.104, Q.128, M.129, E.130 Chain B: H.29, D.32, V.33, N.36, R.39, L.40, R.43 Ligands: EDO.10 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.73, B:D.32 Hydrogen bonds: A:M.66, A:A.67, A:E.130 Water bridges: A:H.131, A:H.131 EBL.7: 18 residues within 4Å: Chain A: H.29, D.32, V.33, N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, F.104, Q.128, M.129, E.130 Ligands: EDO.4 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:D.32, B:Y.73 Hydrogen bonds: B:M.66, B:A.67, B:E.130 Water bridges: B:H.131, B:H.131

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: I.87, N.88 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: I.87, N.88 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: R.41, Q.57, F.58, R.59, L.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:Q.57, A:R.59 EDO.4: 3 residues within 4Å: Chain A: N.36, R.39 Ligands: EBL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:R.39, A:R.39 EDO.9: 5 residues within 4Å: Chain B: R.41, Q.57, F.58, R.59, L.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.41, B:R.41, B:Q.57, B:R.59 EDO.10: 3 residues within 4Å: Chain B: N.36, R.39 Ligands: EBL.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.36, B:R.39, B:R.39

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: E.56, P.95, E.96, C.99 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.56 DMS.6: 3 residues within 4Å: Chain A: E.114, I.117, M.118 No protein-ligand interaction detected (PLIP) DMS.11: 4 residues within 4Å: Chain B: E.56, P.95, E.96, C.99 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.56 DMS.12: 3 residues within 4Å: Chain B: E.114, I.117, M.118 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huckvale, R. et al., Improved Binding Affinity and Pharmacokinetics Enable Sustained Degradation of BCL6 In Vivo . J.Med.Chem. (2022)

Release Date

2022-06-15

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

B-cell lymphoma 6 protein

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