Fluorine in PDB 6x85: Crystal Structure of Tnfalpha with Indolinone Compound 9

The structure of Crystal Structure of Tnfalpha with Indolinone Compound 9, PDB code: 6x85 was solved by K.L.Longenecker, V.S.Stoll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.11 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	252.508, 65.672, 54.241, 90, 95.1, 90
R / Rfree (%)	19.8 / 25.2

The binding sites of Fluorine atom in the Crystal Structure of Tnfalpha with Indolinone Compound 9 (pdb code 6x85). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Tnfalpha with Indolinone Compound 9, PDB code: 6x85:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Tnfalpha with Indolinone Compound 9


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 Tnfalpha with Indolinone Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:56.9 occ:1.00 F1 B:UTV901 0.0 56.9 1.0 C10 B:UTV901 1.4 61.3 1.0 F B:UTV901 2.1 60.6 1.0 O B:UTV901 2.2 63.4 1.0 CD1 C:ILE155 3.1 78.6 1.0 C9 B:UTV901 3.1 62.9 1.0 CD1 B:LEU57 3.2 64.2 1.0 C8 B:UTV901 3.3 59.3 1.0 CD2 C:TYR59 3.4 44.2 1.0 CE2 C:TYR59 3.6 43.5 1.0 CG1 C:ILE155 3.9 67.4 1.0 CD2 C:LEU57 4.1 59.7 1.0 CG C:TYR59 4.2 45.0 1.0 CB C:LEU57 4.3 55.1 1.0 C4 B:UTV901 4.4 62.1 1.0 CG C:LEU57 4.4 59.3 1.0 CG B:LEU57 4.5 63.0 1.0 CZ C:TYR59 4.6 50.1 1.0 CD2 B:LEU57 4.6 63.7 1.0 C7 B:UTV901 4.7 56.6 1.0 CB C:TYR59 4.7 45.8 1.0 CA B:GLY122 4.9 46.6 1.0 CB C:ILE155 4.9 66.3 1.0 N B:GLY122 4.9 46.8 1.0 C3 B:UTV901 5.0 62.9 1.0 OH C:TYR119 5.0 51.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Tnfalpha with Indolinone Compound 9


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 Tnfalpha with Indolinone Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:60.6 occ:1.00 F B:UTV901 0.0 60.6 1.0 C10 B:UTV901 1.3 61.3 1.0 O B:UTV901 2.1 63.4 1.0 F1 B:UTV901 2.1 56.9 1.0 CD1 B:LEU57 2.9 64.2 1.0 N B:GLY122 3.0 46.8 1.0 C B:GLY121 3.1 51.0 1.0 C9 B:UTV901 3.3 62.9 1.0 O B:GLY121 3.4 50.9 1.0 CA B:GLY122 3.4 46.6 1.0 CA B:GLY121 3.6 48.1 1.0 OH C:TYR119 3.7 51.7 1.0 C B:GLY122 4.0 51.4 1.0 CD2 C:TYR59 4.0 44.2 1.0 C3 B:UTV901 4.0 62.9 1.0 CE2 C:TYR59 4.1 43.5 1.0 C4 B:UTV901 4.1 62.1 1.0 CG C:TYR59 4.3 45.0 1.0 C8 B:UTV901 4.3 59.3 1.0 O B:GLY122 4.3 50.9 1.0 CG B:LEU57 4.3 63.0 1.0 O B:ILE58 4.3 56.6 1.0 CZ C:TYR59 4.4 50.1 1.0 CD1 C:ILE155 4.5 78.6 1.0 CD1 C:TYR59 4.6 46.1 1.0 CE1 C:TYR59 4.7 45.0 1.0 N B:VAL123 4.7 50.3 1.0 CB C:TYR59 4.8 45.8 1.0 CD2 B:LEU57 4.9 63.7 1.0 N B:GLY121 4.9 49.4 1.0

J.D.Dietrich, K.L.Longenecker, N.S.Wilson, C.Goess, S.C.Panchal, S.L.Swann, A.M.Petros, A.D.Hobson, D.Ihle, D.Song, P.Richardson, K.M.Comess, P.B.Cox, A.Dombrowski, K.Sarris, D.L.Donnelly-Roberts, D.B.Duignan, A.Gomtsyan, P.Jung, A.C.Krueger, S.Mathieu, A.Mcclure, V.S.Stoll, J.Wetter, J.A.Mankovich, P.J.Hajduk, A.Vasudevan, R.H.Stoffel, C.Sun. Development of Orally Efficacious Allosteric Inhibitors of Tnf Alpha Via Fragment-Based Drug Design. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33378180
DOI: 10.1021/ACS.JMEDCHEM.0C01280