Fluorine in PDB 6tq9: Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124, PDB code: 6tq9 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)	44.71 / 2.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.365, 147.067, 72.536, 90.00, 111.09, 90.00
R / Rfree (%)	24 / 26.9

The binding sites of Fluorine atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124 (pdb code 6tq9). 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 Sb-408124, PDB code: 6tq9:
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 Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:62.6 occ:1.00 F1 A:NVN401 0.0 62.6 1.0 C6 A:NVN401 1.4 51.3 1.0 C7 A:NVN401 2.3 48.0 1.0 C5 A:NVN401 2.3 57.0 1.0 OG A:SER103 2.4 84.7 1.0 H4 A:NVN401 2.5 70.0 1.0 H5 A:NVN401 2.5 59.2 1.0 OH A:TYR348 2.8 82.8 1.0 CB A:CYS99 3.3 49.5 1.0 O A:CYS99 3.3 80.7 1.0 H4 A:NVN402 3.5 0.8 1.0 C4 A:NVN401 3.6 72.3 1.0 C5 A:NVN402 3.6 90.2 1.0 C8 A:NVN401 3.6 63.5 1.0 C A:CYS99 3.7 66.8 1.0 CB A:SER103 3.7 73.5 1.0 CA A:CYS99 3.8 57.8 1.0 C4 A:NVN402 3.8 98.2 1.0 F2 A:NVN402 3.9 96.1 1.0 CG2 A:ILE122 3.9 96.0 1.0 C3 A:NVN401 4.1 74.5 1.0 CZ A:TYR348 4.1 69.9 1.0 N A:SER103 4.2 75.9 1.0 C6 A:NVN402 4.2 75.4 1.0 CA A:SER103 4.2 66.2 1.0 CB A:GLN126 4.3 52.7 1.0 CG A:GLN126 4.5 55.2 1.0 H7 A:NVN401 4.5 78.0 1.0 C3 A:NVN402 4.5 94.1 1.0 N A:LEU100 4.6 63.6 1.0 SG A:CYS99 4.6 53.7 1.0 F1 A:NVN402 4.6 77.2 1.0 F2 A:NVN401 4.7 86.5 1.0 C9 A:NVN401 4.8 68.2 1.0 C7 A:NVN402 4.9 74.7 1.0 CE2 A:TYR348 4.9 62.1 1.0 CB A:ALA102 5.0 72.6 1.0 C A:ALA102 5.0 66.1 1.0 CE1 A:TYR348 5.0 61.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:86.5 occ:1.00 F2 A:NVN401 0.0 86.5 1.0 C4 A:NVN401 1.3 72.3 1.0 C5 A:NVN401 2.3 57.0 1.0 C3 A:NVN401 2.4 74.5 1.0 H4 A:NVN401 2.5 70.0 1.0 N1 A:NVN401 2.8 80.5 1.0 CZ3 A:TRP112 2.9 52.8 1.0 CG2 A:VAL106 3.4 74.6 1.0 C6 A:NVN401 3.6 51.3 1.0 CE3 A:TRP112 3.6 55.6 1.0 C8 A:NVN401 3.7 63.5 1.0 CH2 A:TRP112 3.9 65.2 1.0 C2 A:NVN401 4.1 72.8 1.0 C7 A:NVN401 4.1 48.0 1.0 H2 A:NVN402 4.2 0.9 1.0 O A:ALA102 4.2 67.9 1.0 CB A:VAL106 4.2 58.0 1.0 F2 A:NVN402 4.5 96.1 1.0 N1 A:NVN402 4.5 89.6 1.0 C A:ALA102 4.6 66.1 1.0 CG1 A:VAL106 4.7 59.8 1.0 F1 A:NVN401 4.7 62.6 1.0 H3 A:NVN401 4.7 79.8 1.0 CB A:ALA102 4.7 72.6 1.0 CG2 A:ILE122 4.8 96.0 1.0 C9 A:NVN401 4.8 68.2 1.0 CA A:SER103 4.9 66.2 1.0 N A:SER103 4.9 75.9 1.0 C1 A:NVN401 5.0 65.1 1.0 C10 A:NVN401 5.0 72.5 1.0 C1 A:NVN402 5.0 83.5 1.0 CD2 A:TRP112 5.0 50.4 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:77.2 occ:1.00 F1 A:NVN402 0.0 77.2 1.0 C6 A:NVN402 1.4 75.4 1.0 C5 A:NVN402 2.3 90.2 1.0 C7 A:NVN402 2.3 74.7 1.0 H4 A:NVN402 2.5 0.8 1.0 H5 A:NVN402 2.5 91.2 1.0 OH A:TYR348 3.6 82.8 1.0 C4 A:NVN402 3.6 98.2 1.0 C8 A:NVN402 3.6 83.7 1.0 CZ A:TYR348 3.7 69.9 1.0 NE2 A:GLN126 3.8 77.0 1.0 CE2 A:TYR348 3.8 62.1 1.0 O1 A:NVN402 3.8 84.1 1.0 CB A:VAL347 3.8 59.7 1.0 CG1 A:VAL347 3.9 60.9 1.0 O A:HIS344 3.9 69.1 1.0 CG2 A:VAL347 4.0 66.9 1.0 CD A:GLN126 4.1 71.2 1.0 C3 A:NVN402 4.1 94.1 1.0 CA A:HIS344 4.3 57.4 1.0 OE1 A:GLN126 4.4 79.8 1.0 CB A:HIS344 4.4 52.0 1.0 H5 A:NVN401 4.4 59.2 1.0 CE1 A:TYR348 4.5 61.6 1.0 OG A:SER103 4.6 84.7 1.0 CD2 A:TYR348 4.6 60.4 1.0 C A:HIS344 4.6 63.3 1.0 F1 A:NVN401 4.6 62.6 1.0 F2 A:NVN402 4.7 96.1 1.0 CG A:GLN126 4.7 55.2 1.0 C11 A:NVN402 4.8 86.6 1.0 CG A:HIS344 4.9 56.0 1.0 C9 A:NVN402 4.9 87.6 1.0 C7 A:NVN401 4.9 48.0 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:96.1 occ:1.00 F2 A:NVN402 0.0 96.1 1.0 C4 A:NVN402 1.3 98.2 1.0 C5 A:NVN402 2.3 90.2 1.0 C3 A:NVN402 2.4 94.1 1.0 H4 A:NVN402 2.5 0.8 1.0 N1 A:NVN402 2.7 89.6 1.0 CB A:SER103 3.0 73.5 1.0 OG A:SER103 3.1 84.7 1.0 CA A:SER103 3.2 66.2 1.0 C5 A:NVN401 3.5 57.0 1.0 H4 A:NVN401 3.6 70.0 1.0 C6 A:NVN402 3.6 75.4 1.0 C6 A:NVN401 3.6 51.3 1.0 C8 A:NVN402 3.7 83.7 1.0 ND1 A:HIS344 3.7 56.2 1.0 O A:SER103 3.7 71.4 1.0 C4 A:NVN401 3.9 72.3 1.0 F1 A:NVN401 3.9 62.6 1.0 C A:SER103 3.9 75.4 1.0 C2 A:NVN402 4.1 87.4 1.0 CG A:HIS344 4.1 56.0 1.0 C7 A:NVN402 4.1 74.7 1.0 C7 A:NVN401 4.2 48.0 1.0 CB A:HIS344 4.2 52.0 1.0 N A:SER103 4.3 75.9 1.0 OD2 A:ASP107 4.4 59.0 1.0 CE1 A:HIS344 4.4 58.7 1.0 C3 A:NVN401 4.4 74.5 1.0 F2 A:NVN401 4.5 86.5 1.0 C8 A:NVN401 4.6 63.5 1.0 OH A:TYR348 4.6 82.8 1.0 H5 A:NVN401 4.6 59.2 1.0 H2 A:NVN402 4.6 0.9 1.0 F1 A:NVN402 4.7 77.2 1.0 C9 A:NVN402 4.8 87.6 1.0 CD2 A:HIS344 4.9 57.6 1.0 C1 A:NVN402 4.9 83.5 1.0 C10 A:NVN402 5.0 89.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:0.8 occ:1.00 F1 B:NVN401 0.0 0.8 1.0 C6 B:NVN401 1.4 0.7 1.0 C7 B:NVN401 2.3 0.8 1.0 C5 B:NVN401 2.4 0.0 1.0 H4 B:NVN401 2.5 0.8 1.0 H5 B:NVN401 2.5 0.3 1.0 OG B:SER103 2.8 68.4 1.0 OH B:TYR348 3.2 85.4 1.0 CB B:CYS99 3.4 55.1 1.0 C4 B:NVN401 3.6 0.6 1.0 C8 B:NVN401 3.6 0.9 1.0 O B:CYS99 3.7 78.2 1.0 CG2 B:ILE122 3.8 54.0 1.0 CA B:CYS99 4.0 61.9 1.0 C B:CYS99 4.1 72.0 1.0 C3 B:NVN401 4.1 0.0 1.0 CB B:SER103 4.1 71.1 1.0 CB B:GLN126 4.2 55.0 1.0 N B:SER103 4.3 75.6 1.0 H7 B:NVN401 4.4 0.9 1.0 SG B:CYS99 4.5 53.7 1.0 CB B:ALA102 4.5 58.0 1.0 CZ B:TYR348 4.5 72.2 1.0 CA B:SER103 4.6 68.4 1.0 O B:ILE122 4.6 63.7 1.0 CG B:GLN126 4.6 56.4 1.0 F2 B:NVN401 4.7 0.3 1.0 C9 B:NVN401 4.8 0.6 1.0 C B:ALA102 4.9 69.9 1.0 C B:ILE122 5.0 55.9 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Orexin-1 Receptor in Complex with Sb-408124


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 Sb-408124 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:0.3 occ:1.00 F2 B:NVN401 0.0 0.3 1.0 C4 B:NVN401 1.3 0.6 1.0 C5 B:NVN401 2.3 0.0 1.0 C3 B:NVN401 2.4 0.0 1.0 H4 B:NVN401 2.5 0.8 1.0 N1 B:NVN401 2.8 99.5 1.0 CG2 B:VAL106 3.2 77.6 1.0 CG1 B:VAL106 3.4 55.1 1.0 CB B:VAL106 3.5 64.6 1.0 C6 B:NVN401 3.6 0.7 1.0 CZ3 B:TRP112 3.6 61.8 1.0 C8 B:NVN401 3.7 0.9 1.0 CE3 B:TRP112 4.0 66.6 1.0 C2 B:NVN401 4.1 0.0 1.0 C7 B:NVN401 4.1 0.8 1.0 O B:ALA102 4.4 66.0 1.0 H3 B:NVN401 4.7 1.0 1.0 F1 B:NVN401 4.7 0.8 1.0 CA B:SER103 4.7 68.4 1.0 C9 B:NVN401 4.8 0.6 1.0 CH2 B:TRP112 4.8 68.0 1.0 C B:ALA102 4.9 69.9 1.0 OG B:SER103 4.9 68.4 1.0 C1 B:NVN401 4.9 97.0 1.0 C10 B:NVN401 5.0 0.2 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