Fluorine in PDB 6tq6: Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14, PDB code: 6tq6 was solved by M.Rappas, A.Ali, K.A.Bennett, J.D.Brown, S.J.Bucknell, M.Congreve, R.M.Cooke, G.Cseke, C.De Graaf, A.S.Dore, J.C.Errey, A.Jazayeri, F.H.Marshall, J.S.Mason, R.Mould, J.C.Patel, B.G.Tehan, M.Weir, J.A.Christopher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.834, 147.072, 72.260, 90.00, 111.56, 90.00
R / Rfree (%)	22.3 / 26.3

The binding sites of Fluorine atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14 (pdb code 6tq6). 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 Orexin-1 Receptor in Complex with Compound 14, PDB code: 6tq6:
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 Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:97.8 occ:1.00 F1 A:NVH401 0.0 97.8 1.0 C13 A:NVH401 1.4 98.3 0.0 C14 A:NVH401 2.4 99.1 1.0 C18 A:NVH401 2.4 98.0 0.6 OG A:SER315 3.5 46.0 1.0 C15 A:NVH401 3.7 0.9 0.4 C17 A:NVH401 3.7 98.0 1.0 CD2 A:TYR311 3.8 45.0 1.0 CG1 A:VAL130 3.9 39.8 1.0 C16 A:NVH401 4.2 0.7 0.0 CG2 A:ILE314 4.3 36.0 1.0 CE1 A:PHE219 4.4 34.5 1.0 CE2 A:TYR311 4.4 50.7 1.0 OG1 A:THR223 4.6 47.0 1.0 CG2 A:VAL130 4.6 48.3 1.0 CB A:SER315 4.7 43.5 1.0 F2 A:NVH401 4.7 0.2 0.9 F3 A:NVH401 4.8 96.0 1.0 CG A:TYR311 4.8 41.2 1.0 CB A:VAL130 4.9 45.0 1.0 CB A:TYR311 4.9 34.8 1.0 O A:TYR311 4.9 42.1 1.0 CA A:SER315 5.0 47.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:0.2 occ:0.93 F2 A:NVH401 0.0 0.2 0.9 C15 A:NVH401 1.3 0.9 0.4 C14 A:NVH401 2.4 99.1 1.0 C16 A:NVH401 2.4 0.7 0.0 N3 A:NVH401 2.9 0.2 1.0 C12 A:NVH401 2.9 0.3 1.0 C5 A:NVH401 2.9 0.5 1.0 O1 A:NVH401 2.9 0.9 1.0 O A:HOH510 3.1 93.7 1.0 C13 A:NVH401 3.6 98.3 0.0 C17 A:NVH401 3.7 98.0 1.0 C4 A:NVH401 3.7 0.9 1.0 CG A:GLN126 3.9 58.2 1.0 N4 A:NVH401 4.1 0.5 1.0 C18 A:NVH401 4.2 98.0 0.6 O3 A:NVH401 4.3 0.3 1.0 N1 A:NVH401 4.4 0.4 1.0 NE2 A:GLN126 4.4 69.9 1.0 CG1 A:ILE314 4.4 40.6 1.0 CD A:GLN126 4.4 70.9 1.0 C6 A:NVH401 4.5 0.8 1.0 S1 A:NVH401 4.7 0.9 1.0 F1 A:NVH401 4.7 97.8 1.0 F3 A:NVH401 4.8 96.0 1.0 CG2 A:VAL347 4.9 57.1 1.0 CG2 A:ILE314 4.9 36.0 1.0 CG2 A:VAL130 4.9 48.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:96.0 occ:0.99 F3 A:NVH401 0.0 96.0 1.0 C17 A:NVH401 1.3 98.0 1.0 C18 A:NVH401 2.4 98.0 0.6 C16 A:NVH401 2.4 0.7 0.0 N1 A:NVH401 2.7 0.4 1.0 CG A:ASN318 2.8 72.1 1.0 CB A:ASN318 2.8 50.4 1.0 C12 A:NVH401 2.9 0.3 1.0 ND2 A:ASN318 3.0 74.9 1.0 OD1 A:ASN318 3.4 82.0 1.0 C3 A:NVH401 3.5 0.9 1.0 O A:HOH514 3.6 55.6 1.0 O A:ILE314 3.6 49.4 1.0 C13 A:NVH401 3.6 98.3 0.0 C15 A:NVH401 3.7 0.9 0.4 C4 A:NVH401 3.7 0.9 1.0 N3 A:NVH401 3.8 0.2 1.0 C14 A:NVH401 4.1 99.1 1.0 CG1 A:ILE314 4.2 40.6 1.0 C A:ILE314 4.2 45.6 1.0 CA A:ASN318 4.3 46.6 1.0 CA A:SER315 4.4 47.7 1.0 N A:SER315 4.6 45.5 1.0 N A:ASN318 4.7 46.8 1.0 F1 A:NVH401 4.8 97.8 1.0 F2 A:NVH401 4.8 0.2 0.9 C2 A:NVH401 4.8 0.8 1.0 CD1 A:ILE314 4.9 51.8 1.0 O A:SER315 5.0 49.4 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:0.5 occ:0.81 F1 B:NVH401 0.0 0.5 0.8 C13 B:NVH401 1.4 0.2 0.8 C18 B:NVH401 2.4 0.1 0.8 C14 B:NVH401 2.4 0.7 0.8 CD2 B:TYR311 3.6 50.9 1.0 CG1 B:VAL130 3.7 54.0 1.0 C17 B:NVH401 3.7 0.3 0.8 C15 B:NVH401 3.7 0.3 0.8 OG B:SER315 3.9 56.7 1.0 C16 B:NVH401 4.2 0.0 0.8 CE2 B:TYR311 4.2 54.1 1.0 CG2 B:VAL130 4.3 59.0 1.0 CE2 B:PHE219 4.4 40.7 1.0 OG1 B:THR223 4.5 52.2 1.0 CG2 B:ILE314 4.6 43.6 1.0 CB B:VAL130 4.6 55.5 1.0 CG B:TYR311 4.6 44.4 1.0 F2 B:NVH401 4.7 0.1 0.8 F3 B:NVH401 4.7 0.2 0.8 CB B:TYR311 4.8 40.4 1.0 CZ B:PHE219 4.9 39.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:0.1 occ:0.81 F2 B:NVH401 0.0 0.1 0.8 C15 B:NVH401 1.3 0.3 0.8 C14 B:NVH401 2.3 0.7 0.8 C16 B:NVH401 2.4 0.0 0.8 O1 B:NVH401 2.5 0.5 0.8 C5 B:NVH401 2.7 0.6 0.8 N3 B:NVH401 2.9 1.0 0.8 C12 B:NVH401 2.9 0.8 0.8 C13 B:NVH401 3.6 0.2 0.8 C17 B:NVH401 3.7 0.3 0.8 C4 B:NVH401 3.8 0.7 0.8 N4 B:NVH401 3.9 0.4 0.8 C18 B:NVH401 4.1 0.1 0.8 O3 B:NVH401 4.2 0.1 0.8 CG B:GLN126 4.2 71.4 1.0 CG1 B:ILE314 4.3 56.9 1.0 CG2 B:VAL347 4.6 55.1 1.0 C6 B:NVH401 4.6 0.8 0.8 S1 B:NVH401 4.6 0.4 0.8 N1 B:NVH401 4.6 0.7 0.8 F1 B:NVH401 4.7 0.5 0.8 CD B:GLN126 4.7 87.5 1.0 CG2 B:ILE314 4.8 43.6 1.0 F3 B:NVH401 4.8 0.2 0.8 C10 B:NVH401 4.8 0.5 0.8 CG1 B:VAL347 4.9 47.1 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 14


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 Orexin-1 Receptor in Complex with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:0.2 occ:0.81 F3 B:NVH401 0.0 0.2 0.8 C17 B:NVH401 1.3 0.3 0.8 C18 B:NVH401 2.4 0.1 0.8 C16 B:NVH401 2.4 0.0 0.8 N1 B:NVH401 2.5 0.7 0.8 C12 B:NVH401 2.9 0.8 0.8 CG B:ASN318 3.2 75.8 1.0 CB B:ASN318 3.2 63.9 1.0 C3 B:NVH401 3.2 0.9 0.8 ND2 B:ASN318 3.3 73.2 1.0 C4 B:NVH401 3.5 0.7 0.8 O B:HOH509 3.5 55.0 1.0 C13 B:NVH401 3.6 0.2 0.8 C15 B:NVH401 3.7 0.3 0.8 O B:ILE314 3.7 49.8 1.0 N3 B:NVH401 3.8 1.0 0.8 OD1 B:ASN318 3.8 89.8 1.0 CG1 B:ILE314 4.1 56.9 1.0 C14 B:NVH401 4.1 0.7 0.8 C B:ILE314 4.2 50.2 1.0 CA B:SER315 4.3 53.1 1.0 CE2 B:PHE219 4.5 40.7 1.0 C2 B:NVH401 4.5 0.2 0.8 N B:SER315 4.5 49.8 1.0 CA B:ASN318 4.6 57.7 1.0 F1 B:NVH401 4.7 0.5 0.8 C6 B:NVH401 4.8 0.8 0.8 F2 B:NVH401 4.8 0.1 0.8 CD1 B:ILE314 4.9 58.2 1.0 CD2 B:PHE219 4.9 41.3 1.0 O B:SER315 4.9 56.7 1.0 N B:ASN318 4.9 58.1 1.0 CB B:ILE314 4.9 51.7 1.0 CG2 B:ILE314 4.9 43.6 1.0

M.Rappas, A.Ali, K.A.Bennett, J.D.Brown, S.J.Bucknell, M.Congreve, R.M.Cooke, G.Cseke, C.De Graaf, A.S.Dore, J.C.Errey, A.Jazayeri, F.H.Marshall, J.S.Mason, R.Mould, J.C.Patel, B.Tehan, M.Weir, J.A.Christopher. Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-Ray Crystallography and Computational Analysis. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31860301
DOI: 10.1021/ACS.JMEDCHEM.9B01787