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

The structure of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant, PDB code: 6hlo 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)	29.44 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.189, 76.450, 167.124, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.9

The binding sites of Fluorine atom in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant (pdb code 6hlo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant, PDB code: 6hlo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:79.2 occ:1.00 F10 A:GBQ1501 0.0 79.2 1.0 C09 A:GBQ1501 1.4 62.4 1.0 F12 A:GBQ1501 2.1 73.8 1.0 F11 A:GBQ1501 2.1 71.3 1.0 C07 A:GBQ1501 2.5 56.9 1.0 ND2 A:ASN89 2.9 61.8 1.0 C08 A:GBQ1501 3.2 48.6 1.0 C06 A:GBQ1501 3.5 42.0 1.0 CE A:MET295 3.6 69.2 1.0 SD A:MET295 3.8 74.6 1.0 CG A:PRO112 3.9 42.5 1.0 CB A:PRO112 3.9 42.8 1.0 CG A:ASN89 4.3 60.4 1.0 CG A:MET295 4.3 55.5 1.0 CE A:MET81 4.4 77.7 1.0 SD A:MET81 4.4 71.5 1.0 C03 A:GBQ1501 4.5 43.0 1.0 CE A:MET291 4.7 66.3 1.0 C05 A:GBQ1501 4.7 48.3 1.0 CB A:ASN85 4.7 54.3 1.0 CG A:MET81 4.9 58.1 1.0 OD1 A:ASN89 4.9 67.6 1.0

Fluorine binding site 2 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:71.3 occ:1.00 F11 A:GBQ1501 0.0 71.3 1.0 C09 A:GBQ1501 1.4 62.4 1.0 F12 A:GBQ1501 2.1 73.8 1.0 F10 A:GBQ1501 2.1 79.2 1.0 C07 A:GBQ1501 2.5 56.9 1.0 C06 A:GBQ1501 2.8 42.0 1.0 CH2 A:TRP261 3.3 43.1 1.0 CG A:MET295 3.6 55.5 1.0 C08 A:GBQ1501 3.8 48.6 1.0 CE A:MET81 3.8 77.7 1.0 CZ3 A:TRP261 3.9 45.2 1.0 SD A:MET295 4.0 74.6 1.0 CE A:MET295 4.1 69.2 1.0 C05 A:GBQ1501 4.2 48.3 1.0 SD A:MET81 4.3 71.5 1.0 CZ2 A:TRP261 4.4 47.3 1.0 CE2 A:PHE264 4.6 44.2 1.0 CZ A:PHE264 4.6 45.8 1.0 ND2 A:ASN89 4.7 61.8 1.0 CB A:MET295 4.7 44.3 1.0 CB A:PRO112 4.7 42.8 1.0 CB A:ALA294 4.8 42.3 1.0 N A:MET295 4.8 42.1 1.0 CA A:MET295 4.9 42.1 1.0 C03 A:GBQ1501 4.9 43.0 1.0

Fluorine binding site 3 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:73.8 occ:1.00 F12 A:GBQ1501 0.0 73.8 1.0 C09 A:GBQ1501 1.4 62.4 1.0 F11 A:GBQ1501 2.1 71.3 1.0 F10 A:GBQ1501 2.1 79.2 1.0 C07 A:GBQ1501 2.5 56.9 1.0 CE A:MET291 3.0 66.3 1.0 C08 A:GBQ1501 3.1 48.6 1.0 ND2 A:ASN89 3.4 61.8 1.0 C06 A:GBQ1501 3.6 42.0 1.0 CE2 A:PHE264 3.8 44.2 1.0 SD A:MET295 3.9 74.6 1.0 CG A:MET295 3.9 55.5 1.0 CZ A:PHE264 4.1 45.8 1.0 SD A:MET291 4.4 76.7 1.0 CG A:MET291 4.4 65.9 1.0 C03 A:GBQ1501 4.4 43.0 1.0 CG A:ASN89 4.6 60.4 1.0 CE A:MET295 4.6 69.2 1.0 C05 A:GBQ1501 4.8 48.3 1.0 CD2 A:PHE264 4.8 43.4 1.0

Fluorine binding site 4 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:56.3 occ:1.00 F14 A:GBQ1501 0.0 56.3 1.0 C13 A:GBQ1501 1.4 48.7 1.0 F15 A:GBQ1501 2.1 57.8 1.0 F16 A:GBQ1501 2.1 53.7 1.0 C05 A:GBQ1501 2.5 48.3 1.0 C06 A:GBQ1501 3.2 42.0 1.0 CE1 A:PHE264 3.4 46.0 1.0 C04 A:GBQ1501 3.4 45.9 1.0 CD1 A:ILE204 3.6 44.5 1.0 CE1 A:HIS265 3.6 54.0 1.0 CZ3 A:TRP261 3.7 45.2 1.0 CD1 A:PHE264 3.9 43.2 1.0 C34 A:GBQ1501 3.9 54.6 1.0 F37 A:GBQ1501 4.0 58.6 1.0 C33 A:GBQ1501 4.0 51.5 1.0 NE2 A:HIS265 4.1 50.2 1.0 CE3 A:TRP261 4.1 52.4 1.0 CZ A:PHE264 4.3 45.8 1.0 CH2 A:TRP261 4.3 43.1 1.0 C35 A:GBQ1501 4.5 55.4 1.0 C07 A:GBQ1501 4.5 56.9 1.0 ND1 A:HIS265 4.6 48.1 1.0 C32 A:GBQ1501 4.7 45.0 1.0 C03 A:GBQ1501 4.7 43.0 1.0 O A:HOH1641 4.9 47.0 1.0 CG1 A:ILE204 4.9 43.9 1.0

Fluorine binding site 5 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:57.8 occ:1.00 F15 A:GBQ1501 0.0 57.8 1.0 C13 A:GBQ1501 1.4 48.7 1.0 F16 A:GBQ1501 2.1 53.7 1.0 F14 A:GBQ1501 2.1 56.3 1.0 C05 A:GBQ1501 2.5 48.3 1.0 C04 A:GBQ1501 2.9 45.9 1.0 CG1 A:ILE113 3.2 59.1 1.0 CD1 A:ILE204 3.3 44.5 1.0 C35 A:GBQ1501 3.4 55.4 1.0 C34 A:GBQ1501 3.4 54.6 1.0 F37 A:GBQ1501 3.6 58.6 1.0 C06 A:GBQ1501 3.7 42.0 1.0 CA A:ILE113 4.0 46.8 1.0 C36 A:GBQ1501 4.0 46.6 1.0 C33 A:GBQ1501 4.1 51.5 1.0 CB A:ILE113 4.2 48.2 1.0 CD1 A:ILE113 4.2 48.8 1.0 C03 A:GBQ1501 4.3 43.0 1.0 N A:ILE113 4.3 46.2 1.0 C A:PRO112 4.7 45.9 1.0 CG1 A:VAL200 4.7 45.3 1.0 C32 A:GBQ1501 4.7 45.0 1.0 C31 A:GBQ1501 4.7 49.6 1.0 O A:PRO112 4.7 45.3 1.0 CG1 A:ILE204 4.8 43.9 1.0 CE1 A:PHE264 4.8 46.0 1.0 C07 A:GBQ1501 4.9 56.9 1.0 CE1 A:HIS265 4.9 54.0 1.0 CG2 A:ILE113 4.9 44.5 1.0

Fluorine binding site 6 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


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 Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:53.7 occ:1.00 F16 A:GBQ1501 0.0 53.7 1.0 C13 A:GBQ1501 1.4 48.7 1.0 F15 A:GBQ1501 2.1 57.8 1.0 F14 A:GBQ1501 2.1 56.3 1.0 C05 A:GBQ1501 2.5 48.3 1.0 C06 A:GBQ1501 3.0 42.0 1.0 CG1 A:ILE116 3.3 44.3 1.0 O A:PRO112 3.5 45.3 1.0 CD1 A:ILE204 3.6 44.5 1.0 C04 A:GBQ1501 3.6 45.9 1.0 CB A:ILE116 3.7 47.7 1.0 C A:PRO112 3.9 45.9 1.0 CA A:ILE113 4.1 46.8 1.0 CG2 A:ILE116 4.1 40.9 1.0 CH2 A:TRP261 4.2 43.1 1.0 N A:ILE113 4.2 46.2 1.0 CZ3 A:TRP261 4.2 45.2 1.0 C07 A:GBQ1501 4.4 56.9 1.0 CB A:PRO112 4.4 42.8 1.0 CG1 A:ILE113 4.5 59.1 1.0 CA A:PRO112 4.7 45.8 1.0 CD1 A:ILE116 4.7 40.7 1.0 C03 A:GBQ1501 4.8 43.0 1.0 CZ2 A:TRP261 4.9 47.3 1.0 CE3 A:TRP261 5.0 52.4 1.0 CB A:ILE113 5.0 48.2 1.0 CG1 A:ILE204 5.0 43.9 1.0

Fluorine binding site 7 out of 7 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Aprepitant within 5.0Å range: probe atom residue distance (Å) B Occ A:F1501 b:58.6 occ:1.00 F37 A:GBQ1501 0.0 58.6 1.0 C34 A:GBQ1501 1.4 54.6 1.0 C33 A:GBQ1501 2.4 51.5 1.0 C35 A:GBQ1501 2.4 55.4 1.0 CG1 A:VAL200 3.3 45.3 1.0 OG1 A:THR201 3.3 56.2 1.0 CE1 A:HIS265 3.4 54.0 1.0 CD1 A:ILE204 3.5 44.5 1.0 F15 A:GBQ1501 3.6 57.8 1.0 N A:THR201 3.6 46.4 1.0 CA A:THR201 3.6 50.0 1.0 C32 A:GBQ1501 3.7 45.0 1.0 C36 A:GBQ1501 3.7 46.6 1.0 C A:VAL200 3.8 52.6 1.0 ND1 A:HIS265 3.9 48.1 1.0 CB A:VAL200 4.0 46.6 1.0 F14 A:GBQ1501 4.0 56.3 1.0 O A:VAL200 4.0 55.9 1.0 CB A:THR201 4.1 54.7 1.0 CG1 A:ILE204 4.1 43.9 1.0 C31 A:GBQ1501 4.2 49.6 1.0 O A:HOH1632 4.4 59.8 1.0 CD2 A:HIS197 4.4 51.5 1.0 C13 A:GBQ1501 4.5 48.7 1.0 CA A:VAL200 4.5 52.0 1.0 NE2 A:HIS265 4.6 50.2 1.0 O A:HIS197 4.6 56.1 1.0 NE2 A:HIS197 4.7 58.4 1.0 CG2 A:THR201 4.8 50.1 1.0 C A:THR201 5.0 53.7 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