Fluorine in PDB 6tot: Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant, PDB code: 6tot 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)	24.02 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.725, 145.715, 71.703, 90.00, 112.25, 90.00
R / Rfree (%)	20.6 / 23.9

The binding sites of Fluorine atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant (pdb code 6tot). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant, PDB code: 6tot:
Jump to Fluorine binding site number: 1; 2; 3; 4;

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


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 Lemborexant within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:51.4 occ:1.00 F29 A:NRK401 0.0 51.4 1.0 C24 A:NRK401 1.4 49.0 1.0 C25 A:NRK401 2.4 45.2 1.0 C23 A:NRK401 2.4 45.1 1.0 H251 A:NRK401 2.6 45.1 1.0 H231 A:NRK401 2.6 45.1 1.0 H273 A:NRK401 3.1 45.1 1.0 CB A:ALA102 3.6 53.2 1.0 CZ3 A:TRP112 3.6 52.7 1.0 N26 A:NRK401 3.7 48.5 1.0 C22 A:NRK401 3.7 45.2 1.0 N A:SER103 3.7 48.6 1.0 CG2 A:ILE122 3.7 59.2 1.0 OG A:SER103 3.7 56.1 1.0 C A:ALA102 3.8 55.1 1.0 C27 A:NRK401 4.0 45.2 1.0 CH2 A:TRP112 4.0 53.5 1.0 CA A:SER103 4.0 47.6 1.0 O A:ALA102 4.1 55.7 1.0 C21 A:NRK401 4.2 48.4 1.0 C16 A:NRK401 4.3 47.6 1.0 CA A:ALA102 4.3 53.0 1.0 O A:CYS99 4.4 55.3 1.0 N15 A:NRK401 4.4 49.2 1.0 H221 A:NRK401 4.4 45.1 1.0 H271 A:NRK401 4.5 45.1 1.0 CB A:SER103 4.5 50.6 1.0 H272 A:NRK401 4.5 45.1 1.0 CG2 A:VAL106 4.6 50.0 1.0 CE3 A:TRP112 4.8 51.7 1.0 CB A:ILE122 4.9 58.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant


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 Lemborexant within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:56.5 occ:1.00 F30 A:NRK401 0.0 56.5 1.0 C08 A:NRK401 1.3 48.5 1.0 C07 A:NRK401 2.4 45.2 1.0 C09 A:NRK401 2.4 45.2 1.0 H071 A:NRK401 2.5 45.1 1.0 H091 A:NRK401 2.5 45.1 1.0 CG2 A:VAL130 3.3 46.6 1.0 C06 A:NRK401 3.6 47.1 1.0 NE2 A:GLN126 3.6 48.5 1.0 C10 A:NRK401 3.6 45.2 1.0 CE2 A:TYR311 3.8 46.3 1.0 CG2 A:VAL347 3.9 51.7 1.0 OE1 A:GLN126 4.0 61.4 1.0 CD1 A:ILE314 4.0 51.9 1.0 CD2 A:TYR311 4.0 45.3 1.0 CG2 A:ILE314 4.1 41.9 1.0 CG1 A:VAL347 4.1 51.7 1.0 C11 A:NRK401 4.1 45.2 1.0 CD A:GLN126 4.2 62.9 1.0 CG1 A:VAL130 4.3 46.4 1.0 CB A:VAL130 4.4 47.2 1.0 H282 A:NRK401 4.4 45.1 1.0 H101 A:NRK401 4.4 45.1 1.0 CB A:VAL347 4.6 52.0 1.0 CG1 A:ILE314 4.7 41.7 1.0 C03 A:NRK401 4.8 47.3 1.0 CZ A:TYR311 4.9 56.0 1.0 H011 A:NRK401 5.0 45.1 1.0 CB A:ILE314 5.0 42.1 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Orexin-1 Receptor in Complex with Lemborexant


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 Lemborexant within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:49.8 occ:1.00 F29 B:NRK401 0.0 49.8 1.0 C24 B:NRK401 1.4 47.7 1.0 C25 B:NRK401 2.4 45.2 1.0 C23 B:NRK401 2.4 45.1 1.0 H251 B:NRK401 2.5 45.1 1.0 H231 B:NRK401 2.7 45.1 1.0 H273 B:NRK401 2.9 45.1 1.0 CB B:ALA102 3.4 49.0 1.0 CZ3 B:TRP112 3.4 44.7 1.0 N B:SER103 3.5 48.8 1.0 C B:ALA102 3.5 53.6 1.0 OG B:SER103 3.5 58.1 1.0 N26 B:NRK401 3.6 48.5 1.0 C22 B:NRK401 3.7 45.1 1.0 CA B:SER103 3.8 48.0 1.0 O B:ALA102 3.9 55.0 1.0 C27 B:NRK401 3.9 45.1 1.0 CH2 B:TRP112 4.0 45.4 1.0 CA B:ALA102 4.1 49.0 1.0 CG2 B:ILE122 4.1 52.0 1.0 C21 B:NRK401 4.2 47.9 1.0 CG2 B:VAL106 4.2 53.9 1.0 CB B:SER103 4.3 51.5 1.0 H271 B:NRK401 4.3 45.1 1.0 C16 B:NRK401 4.4 45.6 1.0 H272 B:NRK401 4.4 45.1 1.0 O B:CYS99 4.4 58.0 1.0 H221 B:NRK401 4.4 45.1 1.0 CE3 B:TRP112 4.5 44.0 1.0 N15 B:NRK401 4.6 47.2 1.0 CB B:VAL106 5.0 54.0 1.0

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


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 Lemborexant within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:51.3 occ:1.00 F30 B:NRK401 0.0 51.3 1.0 C08 B:NRK401 1.4 47.8 1.0 C07 B:NRK401 2.4 45.2 1.0 C09 B:NRK401 2.4 45.2 1.0 H071 B:NRK401 2.5 45.1 1.0 H091 B:NRK401 2.6 45.1 1.0 CG2 B:VAL130 3.2 46.3 1.0 CE2 B:TYR311 3.4 44.6 1.0 CG2 B:VAL347 3.5 51.5 1.0 OE1 B:GLN126 3.6 75.4 1.0 C06 B:NRK401 3.7 46.3 1.0 C10 B:NRK401 3.7 45.2 1.0 NE2 B:GLN126 3.7 51.0 1.0 CD2 B:TYR311 3.8 43.7 1.0 CG1 B:VAL347 3.8 50.8 1.0 H282 B:NRK401 4.1 45.1 1.0 CD B:GLN126 4.1 70.0 1.0 C11 B:NRK401 4.2 45.2 1.0 CG1 B:VAL130 4.2 45.9 1.0 CD1 B:ILE314 4.2 56.3 1.0 CB B:VAL130 4.3 46.3 1.0 CB B:VAL347 4.3 51.4 1.0 CG2 B:ILE314 4.3 47.1 1.0 H101 B:NRK401 4.4 45.1 1.0 CZ B:TYR311 4.6 54.2 1.0 C03 B:NRK401 4.9 47.0 1.0 OH B:TYR311 4.9 59.3 1.0 C28 B:NRK401 5.0 45.1 1.0 H011 B:NRK401 5.0 45.1 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