Fluorine in PDB 6hlp: Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant

The structure of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant, PDB code: 6hlp was solved by J.Schoppe, J.Ehrenmann, C.Klenk, P.Rucktooa, M.Schutz, A.S.Dore, A.Pluckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.24 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.658, 76.571, 166.035, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.5

The binding sites of Fluorine atom in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant (pdb code 6hlp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant, PDB code: 6hlp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:54.6 occ:1.00 F28 A:GAW1501 0.0 54.6 1.0 C27 A:GAW1501 1.3 54.4 1.0 F29 A:GAW1501 2.1 54.1 1.0 F30 A:GAW1501 2.1 58.5 1.0 C25 A:GAW1501 2.4 47.8 1.0 ND2 A:ASN89 3.0 63.7 1.0 C26 A:GAW1501 3.1 43.6 1.0 C24 A:GAW1501 3.4 44.1 1.0 SD A:MET295 3.4 68.2 1.0 CB A:PRO112 3.6 42.9 1.0 CG A:PRO112 3.7 41.6 1.0 O A:HOH1646 3.8 55.4 1.0 CE A:MET295 4.2 70.0 1.0 CG A:ASN89 4.2 59.1 1.0 C21 A:GAW1501 4.4 44.3 1.0 SD A:MET81 4.4 57.1 1.0 C23 A:GAW1501 4.6 44.0 1.0 CE A:MET81 4.6 60.0 1.0 OD1 A:ASN89 4.8 60.9 1.0 CB A:ASN85 4.8 43.4 1.0 CG A:MET81 4.9 52.6 1.0 CA A:PRO112 5.0 39.1 1.0 C22 A:GAW1501 5.0 42.9 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:54.1 occ:1.00 F29 A:GAW1501 0.0 54.1 1.0 C27 A:GAW1501 1.3 54.4 1.0 F30 A:GAW1501 2.1 58.5 1.0 F28 A:GAW1501 2.1 54.6 1.0 C25 A:GAW1501 2.4 47.8 1.0 C24 A:GAW1501 2.8 44.1 1.0 SD A:MET295 3.2 68.2 1.0 CH2 A:TRP261 3.4 36.8 1.0 C26 A:GAW1501 3.7 43.6 1.0 CZ3 A:TRP261 3.9 37.7 1.0 C23 A:GAW1501 4.1 44.0 1.0 CZ A:PHE264 4.2 41.4 1.0 CE2 A:PHE264 4.2 42.1 1.0 CE A:MET81 4.3 60.0 1.0 CG A:MET295 4.5 56.9 1.0 CZ2 A:TRP261 4.5 38.2 1.0 CE A:MET295 4.6 70.0 1.0 ND2 A:ASN89 4.6 63.7 1.0 SD A:MET81 4.7 57.1 1.0 CB A:PRO112 4.7 42.9 1.0 CB A:ALA294 4.8 38.3 1.0 C21 A:GAW1501 4.9 44.3 1.0 CE1 A:PHE264 5.0 41.6 1.0 C22 A:GAW1501 5.0 42.9 1.0 CD2 A:PHE264 5.0 39.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:58.5 occ:1.00 F30 A:GAW1501 0.0 58.5 1.0 C27 A:GAW1501 1.3 54.4 1.0 F29 A:GAW1501 2.1 54.1 1.0 F28 A:GAW1501 2.1 54.6 1.0 C25 A:GAW1501 2.4 47.8 1.0 C26 A:GAW1501 3.0 43.6 1.0 ND2 A:ASN89 3.5 63.7 1.0 C24 A:GAW1501 3.5 44.1 1.0 SD A:MET295 3.7 68.2 1.0 CE2 A:PHE264 3.9 42.1 1.0 CZ A:PHE264 4.0 41.4 1.0 SD A:MET291 4.1 59.2 1.0 CG A:MET291 4.2 49.5 1.0 C21 A:GAW1501 4.4 44.3 1.0 O A:HOH1646 4.4 55.4 1.0 CG A:ASN89 4.4 59.1 1.0 C23 A:GAW1501 4.7 44.0 1.0 CG A:MET295 4.8 56.9 1.0 CB A:ASN89 4.9 53.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:48.3 occ:1.00 F32 A:GAW1501 0.0 48.3 1.0 C31 A:GAW1501 1.3 47.2 1.0 F33 A:GAW1501 2.1 49.5 1.0 F34 A:GAW1501 2.1 50.2 1.0 C23 A:GAW1501 2.4 44.0 1.0 C24 A:GAW1501 3.0 44.1 1.0 CE1 A:PHE264 3.4 41.6 1.0 C22 A:GAW1501 3.5 42.9 1.0 CZ3 A:TRP261 3.5 37.7 1.0 CD1 A:ILE204 3.7 37.9 1.0 CE1 A:HIS265 3.7 41.5 1.0 C05 A:GAW1501 3.9 52.5 1.0 C04 A:GAW1501 3.9 54.1 1.0 CD1 A:PHE264 4.0 37.6 1.0 CE3 A:TRP261 4.1 39.6 1.0 CH2 A:TRP261 4.1 36.8 1.0 CZ A:PHE264 4.2 41.4 1.0 C25 A:GAW1501 4.3 47.8 1.0 NE2 A:HIS265 4.4 40.0 1.0 ND1 A:HIS265 4.6 41.4 1.0 C21 A:GAW1501 4.7 44.3 1.0 C06 A:GAW1501 4.8 50.0 1.0 C03 A:GAW1501 4.8 52.3 1.0 O A:HOH1661 4.9 36.6 1.0 C26 A:GAW1501 5.0 43.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:49.5 occ:1.00 F33 A:GAW1501 0.0 49.5 1.0 C31 A:GAW1501 1.3 47.2 1.0 F34 A:GAW1501 2.1 50.2 1.0 F32 A:GAW1501 2.1 48.3 1.0 C23 A:GAW1501 2.4 44.0 1.0 C22 A:GAW1501 2.8 42.9 1.0 C04 A:GAW1501 3.0 54.1 1.0 C03 A:GAW1501 3.4 52.3 1.0 CD1 A:ILE204 3.5 37.9 1.0 C05 A:GAW1501 3.6 52.5 1.0 CG1 A:ILE113 3.6 45.1 1.0 C24 A:GAW1501 3.7 44.1 1.0 C21 A:GAW1501 4.2 44.3 1.0 C02 A:GAW1501 4.3 52.5 1.0 C06 A:GAW1501 4.4 50.0 1.0 CG1 A:VAL200 4.4 39.3 1.0 CD1 A:ILE113 4.5 45.7 1.0 CA A:ILE113 4.5 37.5 1.0 CB A:ILE113 4.6 44.4 1.0 CE1 A:HIS265 4.7 41.5 1.0 C07 A:GAW1501 4.7 51.3 1.0 CE1 A:PHE264 4.8 41.6 1.0 C25 A:GAW1501 4.8 47.8 1.0 CG1 A:ILE204 4.8 37.3 1.0 N A:ILE113 4.8 40.9 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:50.2 occ:1.00 F34 A:GAW1501 0.0 50.2 1.0 C31 A:GAW1501 1.3 47.2 1.0 F33 A:GAW1501 2.1 49.5 1.0 F32 A:GAW1501 2.1 48.3 1.0 C23 A:GAW1501 2.4 44.0 1.0 C24 A:GAW1501 3.0 44.1 1.0 C22 A:GAW1501 3.5 42.9 1.0 CD1 A:ILE204 3.5 37.9 1.0 O A:PRO112 3.6 36.5 1.0 CG1 A:ILE116 3.7 40.8 1.0 C A:PRO112 3.8 43.1 1.0 CA A:ILE113 3.9 37.5 1.0 CB A:ILE116 4.0 40.0 1.0 N A:ILE113 4.0 40.9 1.0 CG1 A:ILE113 4.2 45.1 1.0 C25 A:GAW1501 4.3 47.8 1.0 CB A:PRO112 4.4 42.9 1.0 CH2 A:TRP261 4.5 36.8 1.0 CG2 A:ILE116 4.5 35.6 1.0 CZ3 A:TRP261 4.6 37.7 1.0 C21 A:GAW1501 4.7 44.3 1.0 CA A:PRO112 4.7 39.1 1.0 CB A:ILE113 4.7 44.4 1.0 C04 A:GAW1501 4.9 54.1 1.0 CG1 A:ILE204 4.9 37.3 1.0 C26 A:GAW1501 5.0 43.6 1.0

J.Schoppe, J.Ehrenmann, C.Klenk, P.Rucktooa, M.Schutz, A.S.Dore, A.Pluckthun. Crystal Structures of the Human Neurokinin 1 Receptor in Complex with Clinically Used Antagonists. Nat Commun V. 10 17 2019.
ISSN: ESSN 2041-1723
PubMed: 30604743
DOI: 10.1038/S41467-018-07939-8