6HLP: Neurokinin 1 receptor

Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Netupitant. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Pyrococcus abyssi GE5
Chains: 1
Atoms: 4,396
Mol. weight: 67.5 kDa
Ligands: OLC, OLA, CIT, GAW
Released: 16 Jan 2019

Explore 6HLP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HLP contains 22 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	29-58	30
α-helix	61-63	3
α-helix	66-94	29
α-helix	102-135	34
α-helix	144-168	25
β-strand	169-173	5	1
β-strand	178-182	5	1
α-helix	184-186	3
α-helix	191-201	11
α-helix	202-206	5
α-helix	207-225	19
α-helix	1226-1228	3
α-helix	1233-1243	11
β-strand	1250-1255	6	2
β-strand	1258	1	3
α-helix	1265-1275	11
α-helix	1279-1283	5
β-strand	1284-1289	6	2
β-strand	1292	1	3
α-helix	1294-1306	13
β-strand	1310-1313	4	2
α-helix	1319-1326	8
β-strand	1331-1334	4	2
α-helix	1343-1350	8
α-helix	1353	1
β-strand	1354-1358	5	2
α-helix	1361-1366	6
β-strand	1373-1375	3	2
α-helix	1380-1394	15
α-helix	1399-273	51
α-helix	283-308	26
α-helix	310-319	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Substance-P receptor,Substance-P receptor	A	protein	520	Homo sapiens, Pyrococcus abyssi GE5	P25103 (AlphaFold model), Q9V2J8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HLP_1 Substance-P receptor,Substance-P receptor (chains A)
MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAH
KRMRTVTNYFLVNAAFAEASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAIFASI
YSMTAVAFDRYMAIIHPLQPRLSLTATKVVICVIWVLALLLAFPQGYYSTTETMPSRVVC
KIEWPEHPNKIYEKVYHICVTVLIYFLPLLVIGYLYTVVGITLRASGIDCSFWNESYLTG
SRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGK
GDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCL
GAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMS
FSEQVSAARKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLAIMWLAM
SSTMYNPIIYCCLNDRFRLGFKHAFRCCPFISAGDYEGLE

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	7
OLA	Oleic acid	C18 H34 O2	9
CIT	Citric acid	C6 H8 O7	1
GAW	2-[3,5-bis(trifluoromethyl)phenyl]-~{N},2-dimethyl-~{N}-[4-(2-methylphenyl)-6-(…	C30 H32 F6 N4 O	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Schoppe, J., Ehrenmann, J., Klenk, C. et al. Nat Commun (2019) 10:17-17. DOI 10.1038/s41467-018-07939-8 · PubMed

Other PDB entries of the same protein (UniProt P25103 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HLO 2.4 Å, Crystal structure of the Neurokinin 1 receptor in complex with the small molecule…
8U26 2.5 Å, Gaussian Mixture Models based single particle refinement - GPCR (Substance P bound to…
6J20 2.7 Å, Crystal structure of the human NK1 substance P receptor
7P00 2.71 Å, Human Neurokinin 1 receptor (NK1R) substance P Gq chimera (mGsqi) complex
7P02 2.87 Å, Human Neurokinin 1 receptor (NK1R) substance P Gs complex
7RMG 3.0 Å, Substance P bound to active human neurokinin 1 receptor in complex with miniGs/q70
7RMH 3.1 Å, Substance P bound to active human neurokinin 1 receptor in complex with miniGs399
6J21 3.2 Å, Crystal structure of the human NK1 substance P receptor
7RMI 3.2 Å, SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex with…
6HLL 3.27 Å, Crystal structure of the Neurokinin 1 receptor in complex with the small molecule…
6E59 3.4 Å, Crystal structure of the human NK1 tachykinin receptor
2KS9 Solution conformation of substance P in water complexed with NK1R

Browse structure collections

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