SMTL ID : 6zhc.1

PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x QL8: 2-[8-(1,3-benzothiazol-2-ylcarbamoyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]-5-[3-[4-[3-[2-[2-[2-[2-[2-[3-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]prop-1-ynyl]phenoxy]propyl]-1,3-thiazole-4-carboxylic acid(Non-covalent)

QL8.1: 42 residues within 4Å: Chain A: N.9, R.11, F.18, W.30, F.33, Y.40, P.41, L.43, R.49, I.51, H.52, S.53, Y.54, H.57, W.59 Chain D: A.97, E.100, F.101, R.104, Y.105, R.106, A.108, F.109, S.110, D.111, L.112, T.113, E.133, L.134, R.136, N.140, G.142, R.143, V.145, A.146, S.149, F.150, A.153, L.198, Y.199 Ligands: IOD.15, IOD.39 45 PLIP interactions: 30 interactions with chain D, 15 interactions with chain A Hydrophobic interactions: D:E.100, D:E.100, D:F.101, D:F.101, D:R.104, D:Y.105, D:Y.105, D:Y.105, D:R.106, D:A.108, D:F.109, D:F.109, D:F.109, D:L.112, D:T.113, D:V.145, D:F.150, D:A.153, D:Y.199, D:Y.199, A:W.30, A:I.51, A:I.51, A:Y.54, A:W.59 Hydrogen bonds: D:S.110, D:L.112, D:N.140, A:N.9, A:R.49, A:H.52, A:S.53, A:Y.54 Water bridges: D:G.142, D:R.143, D:R.143, D:Y.199, A:Y.54, A:Y.54, A:Y.54 Salt bridges: D:R.143, A:R.11 pi-Stacking: D:F.109, D:F.150, A:Y.40

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

EDO.2: 6 residues within 4Å: Chain A: Q.15, R.50, N.83, G.86, Q.87, P.88 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: G.35, E.36, P.37, Q.137, L.140 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: R.109, S.110, V.112, K.113 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: R.118, L.120, I.122 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain B: C.89, I.90 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: F.25, R.29, P.38, P.39, D.40 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.20, S.21, T.56, G.58 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: R.68, P.69, Q.70 Chain C: Y.67, P.75 Ligands: EDO.25 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: Q.49, L.50, D.52 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: V.123, L.126 Chain C: M.89, N.92 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: K.56, P.78, A.80 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: E.73, P.75 Ligands: EDO.19 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: D.2, F.4, S.64 Chain C: R.66 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain D: P.86, M.87, A.88, A.89 Ligands: EDO.34 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain D: Q.115, S.126, Q.129, V.130 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain D: Y.124, A.172, W.173, T.176 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain D: P.86, A.89 Ligands: EDO.31 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.24, R.103, Q.106 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:Q.106 Water bridges: A:R.24, A:R.24 GOL.7: 5 residues within 4Å: Chain A: N.73, L.77, F.78, V.79, I.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73, A:V.79 GOL.8: 6 residues within 4Å: Chain A: G.69, L.71, P.96, D.139, R.142 Ligands: IOD.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.139, A:R.142 Water bridges: A:R.62, A:G.69 GOL.9: 4 residues within 4Å: Chain A: I.17, R.50, P.88, F.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 GOL.10: 7 residues within 4Å: Chain A: P.23, R.24, V.25, D.63, G.65, T.66 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.25, A:G.65, A:T.66 Water bridges: A:T.66 GOL.27: 7 residues within 4Å: Chain A: L.71, P.96, V.97 Chain C: Y.67, T.68, N.69, S.70 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.69, C:S.70, C:S.70, A:V.97, A:V.97 GOL.35: 5 residues within 4Å: Chain D: N.132, F.135, G.138, Y.177, H.181 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.138, D:Y.177, D:H.181 GOL.36: 4 residues within 4Å: Chain D: S.18, Y.19, S.22, R.95 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.18, D:S.22, D:R.95, D:R.95 GOL.37: 5 residues within 4Å: Chain D: N.140, W.141, G.142, L.198, Y.199 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.141, D:G.142 Water bridges: D:N.140, D:N.140, D:W.141, D:Y.199, D:Y.199

12 x IOD: IODIDE ION(Non-functional Binders)

IOD.11: 2 residues within 4Å: Chain A: H.67, V.136 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain D: R.136 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: R.55 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: T.99 Ligands: GOL.8 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: I.51, H.52 Ligands: QL8.1 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain B: R.43 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain B: H.10 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain C: R.47, E.48, F.93 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain B: P.96 Ligand excluded by PLIP IOD.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.39: 5 residues within 4Å: Chain A: F.33 Chain D: F.109, S.110, R.136 Ligands: QL8.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, C.W. et al., Structural Insights into PROTAC-Mediated Degradation of Bcl-xL. Acs Chem.Biol. (2020)

Release Date

2020-08-05

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-B: B
Elongin-C: C
Bcl-2-like protein 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Bcl-2-like protein 1

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