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

Protein crystallography data

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

Fluorine Binding Sites:

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 6x85

Go back to Fluorine Binding Sites List in 6x85
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 6x85

Go back to Fluorine Binding Sites List in 6x85
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

Reference:

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
Page generated: Sun Jan 24 15:55:51 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy