SMTL ID : 6hlo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x GBQ: 5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one(Non-covalent)

GBQ.1: 22 residues within 4Å: Chain A: M.81, N.89, H.108, N.109, P.112, I.113, I.116, Q.165, I.182, W.184, E.193, Y.196, H.197, V.200, T.201, I.204, W.446, F.449, H.450, F.453, M.476, M.480 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.112, A:I.113, A:V.200, A:W.446, A:F.449, A:F.453 Hydrogen bonds: A:Q.165, A:E.193 pi-Stacking: A:H.197

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

CIT.2: 4 residues within 4Å: Chain A: G.101, L.102, F.103 Ligands: OLA.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.102, A:F.103

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

OLA.3: 5 residues within 4Å: Chain A: K.106, F.107, F.110, F.111, Y.167 Ligand excluded by PLIP OLA.4: 9 residues within 4Å: Chain A: G.213, Y.216, T.217, R.224, I.436, V.439 Ligands: OLA.5, OLA.6, OLC.20 Ligand excluded by PLIP OLA.5: 5 residues within 4Å: Chain A: I.221, R.224, F.347 Ligands: OLA.4, OLA.8 Ligand excluded by PLIP OLA.6: 2 residues within 4Å: Ligands: OLA.4, OLC.20 Ligand excluded by PLIP OLA.7: 3 residues within 4Å: Chain A: I.135, Y.214 Ligands: OLA.8 Ligand excluded by PLIP OLA.8: 4 residues within 4Å: Chain A: V.218, T.222 Ligands: OLA.5, OLA.7 Ligand excluded by PLIP OLA.9: 3 residues within 4Å: Chain A: M.54, L.58, R.64 Ligand excluded by PLIP OLA.10: 6 residues within 4Å: Chain A: L.447, P.448, I.451, F.452, L.455, I.475 Ligand excluded by PLIP OLA.11: 4 residues within 4Å: Chain A: Q.31, L.34, W.35, A.37 Ligand excluded by PLIP OLA.12: 4 residues within 4Å: Chain A: Y.121, F.128, L.142, L.157 Ligand excluded by PLIP OLA.13: 2 residues within 4Å: Chain A: Y.131, Y.214 Ligand excluded by PLIP OLA.14: 2 residues within 4Å: Chain A: F.103 Ligands: CIT.2 Ligand excluded by PLIP OLA.15: 6 residues within 4Å: Chain A: K.433, T.441, L.478, Y.485, I.489, L.493 Ligand excluded by PLIP OLA.16: 6 residues within 4Å: Chain A: V.41, V.44, T.45, V.48, G.49, F.501 Ligand excluded by PLIP OLA.17: 5 residues within 4Å: Chain A: Y.69, V.72, N.73, K.148, W.155 Ligand excluded by PLIP OLA.18: 5 residues within 4Å: Chain A: V.51, W.55, H.503, R.506 Ligands: OLA.19 Ligand excluded by PLIP OLA.19: 5 residues within 4Å: Chain A: A.504, F.505, C.507 Ligands: OLA.18, OLC.22 Ligand excluded by PLIP

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

OLC.20: 9 residues within 4Å: Chain A: G.220, L.223, R.224, R.429, K.433, I.436, C.440 Ligands: OLA.4, OLA.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.433 Hydrogen bonds: A:G.220, A:R.224, A:R.429 OLC.21: 4 residues within 4Å: Chain A: F.103, Y.104, F.107 Ligands: OLC.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.107 OLC.22: 7 residues within 4Å: Chain A: V.47, A.83, V.88, Y.104, F.505 Ligands: OLA.19, OLC.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.47, A:F.505 Water bridges: A:Y.104

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,GlgA glycogen synthase,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,GlgA glycogen synthase,Substance-P receptor

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