SMTL ID : 6hlp.1

Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Netupitant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GAW: 2-[3,5-bis(trifluoromethyl)phenyl]-~{N},2-dimethyl-~{N}-[4-(2-methylphenyl)-6-(4-methylpiperazin-1-yl)pyridin-3-yl]propanamide(Non-covalent)

GAW.1: 17 residues within 4Å: Chain A: N.89, N.109, P.112, I.113, I.116, Q.165, H.197, V.200, T.201, I.204, W.446, F.449, H.450, F.453, P.456, Y.457, M.480 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.112, A:V.200, A:W.446, A:F.449, A:F.449 Hydrogen bonds: A:Q.165 pi-Stacking: A:H.197, A:F.453 pi-Cation interactions: A:H.197 Halogen bonds: A:P.112

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 6 residues within 4Å: Chain A: G.101, L.102, F.103, T.171 Ligands: PEG.18, PEG.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.102 Hydrogen bonds: A:L.102, A:F.103 Water bridges: A:G.101

9 x OLA: OLEIC ACID(Non-functional Binders)(Non-covalent)

OLA.3: 2 residues within 4Å: Ligands: OLA.4, OLC.12 No protein-ligand interaction detected (PLIP) OLA.4: 11 residues within 4Å: Chain A: G.213, Y.216, T.217, G.220, I.221, R.224, V.439 Ligands: OLA.3, OLC.12, PEG.31, PEG.41 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.216, A:V.439 Salt bridges: A:R.224 OLA.5: 7 residues within 4Å: Chain A: F.103, K.106, F.107, F.110, F.163, G.166, Y.167 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.103, A:K.106, A:F.110, A:F.163, A:Y.167 Hydrogen bonds: A:G.166 Salt bridges: A:K.106 OLA.6: 6 residues within 4Å: Chain A: V.51, A.504, F.505, C.507 Ligands: PEG.27, OLC.40 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.51, A:F.505 OLA.7: 6 residues within 4Å: Chain A: Y.121, T.124, A.125, I.154, L.157, L.203 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.121, A:Y.121, A:T.124, A:I.154, A:L.157, A:L.203 OLA.8: 5 residues within 4Å: Chain A: Y.131, H.136, Y.214 Ligands: OLC.13, OLC.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.214 OLA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLA.10: 4 residues within 4Å: Chain A: T.441, L.478, Y.485 Ligands: OLC.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.441, A:L.478, A:Y.485 OLA.11: 3 residues within 4Å: Chain A: V.195, I.198, C.199 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.195, A:I.198

7 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.12: 14 residues within 4Å: Chain A: G.220, L.223, R.224, R.429, K.433, I.436, V.437, C.440, T.441, I.444 Ligands: OLA.3, OLA.4, OLA.10, PEG.41 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.436, A:I.436, A:V.437, A:I.444 Hydrogen bonds: A:R.224, A:R.429, A:R.429 Salt bridges: A:R.224 OLC.13: 9 residues within 4Å: Chain A: F.128, M.132, H.136, Q.139, L.207, Y.214 Ligands: OLA.8, OLC.15, PEG.36 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:F.128, A:L.207, A:Y.214 Salt bridges: A:H.136 OLC.14: 8 residues within 4Å: Chain A: I.32, A.36, T.40, V.87, F.90, T.91, V.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.32, A:V.87, A:F.90, A:T.91 OLC.15: 8 residues within 4Å: Chain A: Y.131, I.135, H.136, Y.214, V.218 Ligands: OLA.8, OLC.13, OLC.39 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.135, A:V.218, A:V.218 Salt bridges: A:H.136 OLC.16: 6 residues within 4Å: Chain A: V.72, N.73, F.76, K.148, I.151, W.155 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.76, A:W.155, A:W.155 OLC.39: 8 residues within 4Å: Chain A: I.135, P.137, I.221, T.222, F.350, D.374 Ligands: OLC.15, PEG.25 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.221, A:T.222, A:F.350, A:F.350 Hydrogen bonds: A:I.135, A:D.374 OLC.40: 6 residues within 4Å: Chain A: V.51, W.55, H.503, A.504, R.506 Ligands: OLA.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.51, A:W.55 Hydrogen bonds: A:H.503, A:R.506

24 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 6 residues within 4Å: Chain A: M.174, P.175, S.176, R.177, V.179 Ligands: PEG.37 Ligand excluded by PLIP PEG.18: 3 residues within 4Å: Chain A: F.103, K.106 Ligands: CIT.2 Ligand excluded by PLIP PEG.19: 3 residues within 4Å: Chain A: V.88, Y.100 Ligands: PEG.24 Ligand excluded by PLIP PEG.20: 3 residues within 4Å: Chain A: L.160, F.163 Ligands: PEG.33 Ligand excluded by PLIP PEG.21: 4 residues within 4Å: Chain A: A.474, I.475, W.477, L.478 Ligand excluded by PLIP PEG.22: 4 residues within 4Å: Chain A: I.382, E.391, N.394, A.395 Ligand excluded by PLIP PEG.23: 3 residues within 4Å: Chain A: T.171, V.178 Ligands: CIT.2 Ligand excluded by PLIP PEG.24: 5 residues within 4Å: Chain A: F.84, F.103, Y.104, F.107 Ligands: PEG.19 Ligand excluded by PLIP PEG.25: 4 residues within 4Å: Chain A: I.134, D.374, F.421 Ligands: OLC.39 Ligand excluded by PLIP PEG.26: 2 residues within 4Å: Chain A: Q.31, W.35 Ligand excluded by PLIP PEG.27: 2 residues within 4Å: Chain A: V.48 Ligands: OLA.6 Ligand excluded by PLIP PEG.28: 3 residues within 4Å: Chain A: S.426, R.429, K.430 Ligand excluded by PLIP PEG.29: 4 residues within 4Å: Chain A: P.448, I.451, L.455, I.475 Ligand excluded by PLIP PEG.30: 3 residues within 4Å: Chain A: T.45, V.48, F.501 Ligand excluded by PLIP PEG.31: 4 residues within 4Å: Chain A: G.213, Y.214, T.217 Ligands: OLA.4 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain A: S.251, G.254, M.255, D.256 Ligand excluded by PLIP PEG.33: 3 residues within 4Å: Chain A: Y.192, C.199 Ligands: PEG.20 Ligand excluded by PLIP PEG.34: 1 residues within 4Å: Chain A: F.206 Ligand excluded by PLIP PEG.35: 2 residues within 4Å: Chain A: C.491, F.505 Ligand excluded by PLIP PEG.36: 1 residues within 4Å: Ligands: OLC.13 Ligand excluded by PLIP PEG.37: 3 residues within 4Å: Chain A: Y.92, N.96 Ligands: PEG.17 Ligand excluded by PLIP PEG.38: 4 residues within 4Å: Chain A: E.379, K.409, F.410, N.413 Ligand excluded by PLIP PEG.41: 5 residues within 4Å: Chain A: C.440, A.443, I.444 Ligands: OLA.4, OLC.12 Ligand excluded by PLIP PEG.42: 2 residues within 4Å: Chain A: W.30, V.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schoppe, J. et al., Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nat Commun (2019)

Release Date

2019-01-16

Peptides

Substance-P receptor,Substance-P receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Substance-P receptor,Substance-P receptor

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