MolNFT v1 · #153060 · protein

Crystal structure of the human NK1 substance P receptor

6J20 · Substance-P RECEPTOR,ENDOLYSIN: “Crystal structure of the human NK1 substance P receptor”. X-ray diffraction, 1 ligand (GBQ), 3 pockets (best druggability 0.72). MolNFT v1 #153060 on GenesisL1: 3D structure, binding sites and…

PDB: 6J20
Type: protein
Length: 398 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Substance-P RECEPTOR,ENDOLYSIN
EC: 3.2.1.17
UniProt: P25103, D9IEF7
Ligands: GBQ
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Substance-P RECEPTOR,ENDOLYSIN (EC 3.2.1.17)	protein	398	78% helix, 3% strand	P25103, D9IEF7

Ligands and binding sites

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 · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	551	0.72	0.80	36	GBQ
2	111	0.42	0.76	25	empty
3	65	0.35	0.77	15	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6J20 · Crystal structure of the human NK1 substance P receptor · the same entry in another collection · chain A against A, TM-score 1.00
P25103 · AlphaFold monomer V2.0 prediction for substance-P receptor (P25103) · a predicted model of the same protein · chain A against A, TM-score 0.72

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P25103
Every structure of UniProt D9IEF7
Elsewhere: RCSB PDB 6J20 · PDBe 6J20 · UniProt P25103 · UniProt D9IEF7

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