SMTL ID : 6qkk.1 (1 other biounit)

Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

5 x H92: 4-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]benzamide(Non-covalent)

H92.1: 15 residues within 4Å: Chain A: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain B: Y.72, D.94, R.96, V.125, T.127, M.133, I.135 Ligands: PO4.2 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.72, B:V.125, B:V.125, B:V.125, B:M.133, B:I.135, A:Y.110, A:W.164, A:Y.205, A:Y.212 Hydrogen bonds: B:D.94, B:T.127, A:Y.110, A:Y.110 Water bridges: B:I.135, A:K.42 Halogen bonds: B:M.133 H92.8: 15 residues within 4Å: Chain B: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain C: Y.72, D.94, R.96, V.125, T.127, M.133, I.135 Ligands: PO4.13 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:V.125, C:V.125, C:V.125, C:M.133, C:I.135, B:Y.110, B:W.164, B:Y.205, B:Y.212 Hydrogen bonds: C:D.94, C:T.127, B:Y.110, B:Y.110 Water bridges: C:I.135 Halogen bonds: C:M.133 H92.15: 15 residues within 4Å: Chain C: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain D: Y.72, D.94, R.96, V.125, T.127, M.133, I.135 Ligands: PO4.16 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:Y.110, C:Y.205, C:Y.212, D:Y.72, D:V.125, D:V.125, D:V.125, D:M.133, D:I.135 Hydrogen bonds: C:Y.110, D:D.94 Water bridges: D:D.94, D:T.127, D:I.135 Halogen bonds: D:M.133 H92.21: 15 residues within 4Å: Chain D: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain E: Y.72, D.94, R.96, V.125, T.127, M.133, I.135 Ligands: PO4.22 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain E Hydrophobic interactions: D:Y.110, D:Y.205, D:Y.212, E:Y.72, E:V.125, E:V.125, E:V.125, E:M.133, E:I.135 Hydrogen bonds: D:Y.110, E:D.94 Water bridges: E:D.94, E:T.127, E:I.135 Halogen bonds: E:M.133 H92.29: 15 residues within 4Å: Chain A: Y.72, D.94, R.96, V.125, T.127, M.133, I.135 Chain E: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Ligands: PO4.30 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:Y.72, A:V.125, A:V.125, A:V.125, A:M.133, A:I.135, E:Y.110, E:Y.205, E:Y.212 Hydrogen bonds: A:D.94, E:Y.110 Water bridges: A:T.127, A:I.135 Halogen bonds: A:M.133

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: K.42, S.167, E.170, E.210 Chain B: D.94, R.96 Ligands: H92.1 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.94, A:E.170 Water bridges: B:D.94, A:K.42 Salt bridges: B:R.96, A:K.42 PO4.13: 7 residues within 4Å: Chain B: K.42, S.167, E.170, E.210 Chain C: D.94, R.96 Ligands: H92.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.167, C:D.94 Water bridges: B:Y.212 Salt bridges: B:K.42, C:R.96 PO4.16: 7 residues within 4Å: Chain C: K.42, S.167, E.170, E.210 Chain D: D.94, R.96 Ligands: H92.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.170, C:E.170 Salt bridges: C:K.42, D:R.96 PO4.22: 7 residues within 4Å: Chain D: K.42, S.167, E.170, E.210 Chain E: D.94, R.96 Ligands: H92.21 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.210 Salt bridges: D:K.42, E:R.96 PO4.30: 7 residues within 4Å: Chain A: D.94, R.96 Chain E: K.42, S.167, E.170, E.210 Ligands: H92.29 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:D.94, E:E.170 Water bridges: A:D.94, E:K.42 Salt bridges: A:R.96, E:K.42

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

EDO.3: 6 residues within 4Å: Chain A: D.68, R.114, Q.117, R.139, S.141 Chain E: R.114 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: Q.55, S.184, Y.186 Chain E: Y.110, S.111, M.143 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: P.38, W.103, Y.166 Chain B: R.96, I.123 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.109, Y.110, S.111, S.112, M.143 Chain B: Q.55, V.70, L.119 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.114 Chain B: D.68, R.114, Q.117, R.139, S.141 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: M.143 Chain B: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: P.38, W.103, Y.166 Chain C: R.96, I.123 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain B: A.109, Y.110, S.111, S.112, M.143 Chain C: Q.55, V.70, L.119, A.137 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: R.114 Chain C: D.68, R.114, Q.117, R.139, S.141 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: M.143 Chain C: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: P.38, W.103, Y.166 Chain D: R.96, I.123 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain C: A.109, Y.110, S.111, S.112, M.143 Chain D: Q.55, V.70, L.119 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: R.114 Chain D: D.68, R.114, Q.117, R.139, S.141 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: M.143 Chain D: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain D: P.38, W.103, Y.166 Chain E: I.123 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain D: A.109, Y.110, S.111, S.112, W.164 Chain E: Q.55, V.70, L.119, A.137 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain A: Q.55, V.70, L.119, A.137 Chain E: A.109, Y.110, S.111, S.112, M.143 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: R.114 Chain E: D.68, R.114, Q.117, R.139, S.141 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain D: S.111, M.143 Chain E: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: R.96, T.97, I.123 Chain E: W.103, Y.166 Ligand excluded by PLIP

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain A: G.90, N.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.91 NAG.26: 1 residues within 4Å: Chain D: N.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.87

1 x OXL: OXALATE ION(Non-covalent)

OXL.10: 5 residues within 4Å: Chain B: P.45, L.46, T.47, G.168, D.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.46, B:D.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bueno, R.V. et al., Interactions between 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors. Acta Crystallogr.,Sect.D (2022)

Release Date

2020-02-19

Peptides

Soluble acetylcholine receptor: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Soluble acetylcholine receptor

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