SMTL ID : 7okj.1

Crystal structure of human BCL6 BTB domain in complex with compound 12c and its enantiomer 12b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x ALA- TRP- VAL- ILE- PRO- ALA: ALA-TRP-VAL-ILE-PRO-ALA(Non-covalent)

ALA-TRP-VAL-ILE-PRO-ALA.1: 11 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, R.93, L.94, H.115, T.119 Ligands: EDO.11 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.12: 11 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 Ligands: EDO.22 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, A:T.119, B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x VHN: (2S)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide(Non-covalent)

VHN.2: 14 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Chain B: N.20, R.23, L.24, R.27 Ligands: VHZ.3 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.23, A:M.50, A:E.114 Water bridges: B:R.27, B:R.27, A:C.52, A:G.54, A:Q.112 pi-Stacking: A:Y.57 VHN.13: 14 residues within 4Å: Chain A: N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Ligands: VHZ.14 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.50, B:E.114, A:R.23 Water bridges: B:C.52, B:G.54, B:Y.57, B:Q.112, A:R.27 pi-Stacking: B:Y.57

2 x VHZ: (2R)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide(Non-covalent)

VHZ.3: 19 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114, H.115 Chain B: H.13, D.16, V.17, N.20, R.23, L.24, R.27 Ligands: VHN.2, CL.9 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:D.16, B:V.17 Hydrogen bonds: B:D.16, B:N.20, A:M.50, A:A.51, A:E.114, A:H.115 Water bridges: B:H.13, B:H.13, B:R.27, B:R.27, A:Q.112 pi-Stacking: A:Y.57 VHZ.14: 19 residues within 4Å: Chain A: H.13, D.16, V.17, N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114, H.115 Ligands: VHN.13, CL.20 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:M.50, B:A.51, B:E.114, B:H.115, B:H.115, A:N.20 Water bridges: B:Q.112, A:R.27, A:R.27 pi-Stacking: B:Y.57 Hydrophobic interactions: A:D.16, A:V.17

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

EDO.4: 2 residues within 4Å: Chain A: R.97, E.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:G.99 EDO.5: 3 residues within 4Å: Chain A: R.27, D.28, I.29 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.27, A:R.27, A:D.28, A:L.30 EDO.6: 2 residues within 4Å: Chain A: D.74, Y.110 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: E.98, I.101, I.124, S.127 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.98, A:E.98, A:M.102 EDO.8: 2 residues within 4Å: Chain A: Q.41, V.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.41 EDO.11: 5 residues within 4Å: Chain A: I.8 Chain B: F.123 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain B: R.97, E.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.98 Water bridges: B:G.99 EDO.16: 3 residues within 4Å: Chain B: R.27, D.28, I.29 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.27, B:R.27, B:D.28, B:L.30 EDO.17: 2 residues within 4Å: Chain B: D.74, Y.110 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain B: E.98, I.101, I.124, S.127 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.98, B:E.98, B:M.102 EDO.19: 2 residues within 4Å: Chain B: Q.41, V.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.41 EDO.22: 5 residues within 4Å: Chain A: F.123 Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.12, ALA-TRP-VAL-ILE-PRO-ALA.12, ALA-TRP-VAL-ILE-PRO-ALA.12 No protein-ligand interaction detected (PLIP)

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

CL.9: 4 residues within 4Å: Chain A: M.113, H.115, V.116 Ligands: VHZ.3 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: M.113, H.115, V.116 Ligands: VHZ.14 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: L.68, S.69, V.70 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lloyd, M.G. et al., Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket. J.Med.Chem. (2021)

Release Date

2021-12-08

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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