Fluorine in PDB 2az5: Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor

The structure of Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor, PDB code: 2az5 was solved by M.M.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	165.254, 165.254, 63.728, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.8

The binding sites of Fluorine atom in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor (pdb code 2az5). 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 Tnf-Alpha with A Small Molecule Inhibitor, PDB code: 2az5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:35.6 occ:1.00 F9 A:3071 0.0 35.6 1.0 C7 A:3071 1.3 36.8 1.0 F10 A:3071 2.1 36.2 1.0 F8 A:3071 2.2 41.1 1.0 C6 A:3071 2.3 35.0 1.0 C11 A:3071 2.7 33.3 1.0 C5 A:3071 3.5 35.8 1.0 CD2 A:LEU57 3.5 48.0 1.0 CA A:GLY121 3.6 20.6 1.0 N A:GLY122 3.7 17.6 1.0 C A:GLY121 3.8 19.5 1.0 O A:ILE58 4.0 24.6 1.0 C1 A:3071 4.1 32.8 1.0 CB A:TYR59 4.3 23.8 1.0 C20 A:3071 4.4 35.8 1.0 O A:GLY121 4.5 18.9 1.0 CA A:GLY122 4.5 15.8 1.0 C4 A:3071 4.6 35.8 1.0 C A:ILE58 4.8 21.5 1.0 C3 A:3071 4.8 35.9 1.0 O A:GLY122 4.8 20.6 1.0 N A:GLY121 4.9 23.6 1.0 CG A:LEU57 5.0 42.4 1.0 C A:GLY122 5.0 16.9 1.0 CA A:TYR59 5.0 24.8 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:36.2 occ:1.00 F10 A:3071 0.0 36.2 1.0 C7 A:3071 1.3 36.8 1.0 F9 A:3071 2.1 35.6 1.0 F8 A:3071 2.1 41.1 1.0 C6 A:3071 2.3 35.0 1.0 C5 A:3071 2.7 35.8 1.0 CD2 A:LEU57 3.2 48.0 1.0 C11 A:3071 3.5 33.3 1.0 CD2 B:TYR59 4.0 16.6 1.0 C4 A:3071 4.0 35.8 1.0 CE2 B:TYR59 4.1 18.0 1.0 CD1 B:ILE155 4.3 23.8 1.0 N A:GLY122 4.3 17.6 1.0 CG B:TYR59 4.4 20.3 1.0 CA A:GLY122 4.4 15.8 1.0 C A:GLY121 4.5 19.5 1.0 CD1 B:LEU57 4.6 31.5 1.0 CZ B:TYR59 4.6 18.9 1.0 CD2 B:LEU57 4.6 22.7 1.0 CG A:LEU57 4.6 42.4 1.0 C1 A:3071 4.7 32.8 1.0 O A:GLY121 4.8 18.9 1.0 C A:GLY122 4.8 16.9 1.0 CD1 B:TYR59 4.8 21.9 1.0 C3 A:3071 4.8 35.9 1.0 CA A:GLY121 4.9 20.6 1.0 CE1 B:TYR59 4.9 20.2 1.0 CB B:TYR59 5.0 15.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:41.1 occ:1.00 F8 A:3071 0.0 41.1 1.0 C7 A:3071 1.3 36.8 1.0 F10 A:3071 2.1 36.2 1.0 F9 A:3071 2.2 35.6 1.0 C6 A:3071 2.4 35.0 1.0 C A:GLY121 2.6 19.5 1.0 O A:GLY121 2.7 18.9 1.0 N A:GLY122 2.9 17.6 1.0 CA A:GLY121 3.2 20.6 1.0 C5 A:3071 3.2 35.8 1.0 C11 A:3071 3.3 33.3 1.0 CA A:GLY122 3.4 15.8 1.0 CD1 B:TYR59 3.8 21.9 1.0 CE1 B:TYR59 3.9 20.2 1.0 CG B:TYR59 4.0 20.3 1.0 C39 A:3071 4.1 24.8 1.0 CZ B:TYR59 4.2 18.9 1.0 CD2 B:TYR59 4.2 16.6 1.0 N A:GLY121 4.3 23.6 1.0 CE2 B:TYR59 4.3 18.0 1.0 C A:GLY122 4.3 16.9 1.0 C4 A:3071 4.5 35.8 1.0 C1 A:3071 4.6 32.8 1.0 CB B:TYR59 4.7 15.2 1.0 CD2 A:LEU57 4.7 48.0 1.0 C38 A:3071 4.7 24.0 1.0 O A:GLY122 4.7 20.6 1.0 O A:ILE58 4.7 24.6 1.0 C37 A:3071 4.8 22.4 1.0 OH B:TYR59 4.9 20.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:35.2 occ:1.00 F9 C:3072 0.0 35.2 1.0 C7 C:3072 1.3 35.4 1.0 F10 C:3072 2.1 36.7 1.0 F8 C:3072 2.2 42.3 1.0 C6 C:3072 2.3 32.8 1.0 C11 C:3072 2.8 31.9 1.0 CA C:GLY121 3.4 22.8 1.0 C5 C:3072 3.5 33.7 1.0 CD2 C:LEU57 3.6 44.4 1.0 N C:GLY122 3.6 17.9 1.0 C C:GLY121 3.6 18.9 1.0 O C:ILE58 3.9 27.1 1.0 C1 C:3072 4.2 29.4 1.0 CA C:GLY122 4.3 18.6 1.0 O C:GLY121 4.3 19.4 1.0 CB C:TYR59 4.3 23.8 1.0 O C:GLY122 4.6 20.2 1.0 C4 C:3072 4.6 34.6 1.0 C20 C:3072 4.7 33.1 1.0 N C:GLY121 4.7 24.0 1.0 C C:GLY122 4.7 20.9 1.0 C C:ILE58 4.8 22.4 1.0 C3 C:3072 4.9 33.4 1.0 CG C:LEU57 4.9 38.8 1.0 O C:LEU120 5.0 27.2 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:36.7 occ:1.00 F10 C:3072 0.0 36.7 1.0 C7 C:3072 1.3 35.4 1.0 F9 C:3072 2.1 35.2 1.0 F8 C:3072 2.1 42.3 1.0 C6 C:3072 2.3 32.8 1.0 C5 C:3072 2.7 33.7 1.0 CD2 C:LEU57 3.1 44.4 1.0 C11 C:3072 3.5 31.9 1.0 C4 C:3072 4.0 34.6 1.0 CD2 D:TYR59 4.1 20.0 1.0 CD1 D:ILE155 4.2 26.3 1.0 CE2 D:TYR59 4.2 18.8 1.0 CA C:GLY122 4.4 18.6 1.0 N C:GLY122 4.4 17.9 1.0 CG D:TYR59 4.4 19.9 1.0 CD1 D:LEU57 4.5 34.3 1.0 CG C:LEU57 4.6 38.8 1.0 CD2 D:LEU57 4.6 28.8 1.0 C C:GLY121 4.6 18.9 1.0 CZ D:TYR59 4.7 21.1 1.0 C1 C:3072 4.7 29.4 1.0 C C:GLY122 4.8 20.9 1.0 C3 C:3072 4.8 33.4 1.0 CD1 D:TYR59 4.8 22.2 1.0 O C:GLY121 4.9 19.4 1.0 CE1 D:TYR59 5.0 20.0 1.0 CA C:GLY121 5.0 22.8 1.0 O C:GLY122 5.0 20.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Tnf-Alpha with A Small Molecule Inhibitor


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 Tnf-Alpha with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:42.3 occ:1.00 F8 C:3072 0.0 42.3 1.0 C7 C:3072 1.3 35.4 1.0 F10 C:3072 2.1 36.7 1.0 F9 C:3072 2.2 35.2 1.0 C6 C:3072 2.4 32.8 1.0 C C:GLY121 2.8 18.9 1.0 O C:GLY121 2.9 19.4 1.0 N C:GLY122 3.1 17.9 1.0 C5 C:3072 3.1 33.7 1.0 CA C:GLY122 3.3 18.6 1.0 CA C:GLY121 3.4 22.8 1.0 C11 C:3072 3.4 31.9 1.0 CD1 D:TYR59 3.6 22.2 1.0 CE1 D:TYR59 3.7 20.0 1.0 CG D:TYR59 3.8 19.9 1.0 CZ D:TYR59 3.9 21.1 1.0 CD2 D:TYR59 4.0 20.0 1.0 CE2 D:TYR59 4.1 18.8 1.0 C39 C:3072 4.2 23.6 1.0 C C:GLY122 4.3 20.9 1.0 C4 C:3072 4.4 34.6 1.0 N C:GLY121 4.5 24.0 1.0 CD2 C:LEU57 4.5 44.4 1.0 CB D:TYR59 4.5 18.1 1.0 OH D:TYR59 4.7 19.9 1.0 C1 C:3072 4.7 29.4 1.0 O C:GLY122 4.7 20.2 1.0 C38 C:3072 4.8 25.6 1.0 O C:ILE58 4.9 27.1 1.0 C37 C:3072 5.0 23.2 1.0 C3 C:3072 5.0 33.4 1.0 N C:VAL123 5.0 19.0 1.0

M.M.He, A.S.Smith, J.D.Oslob, W.M.Flanagan, A.C.Braisted, A.Whitty, M.T.Cancilla, J.Wang, A.A.Lugovskoy, J.C.Yoburn, A.D.Fung, G.Farrington, J.K.Eldredge, E.S.Day, L.A.Cruz, T.G.Cachero, S.K.Miller, J.E.Friedman, I.C.Choong, B.C.Cunningham. Small-Molecule Inhibition of Tnf-Alpha. Science V. 310 1022 2005.
ISSN: ISSN 0036-8075
PubMed: 16284179
DOI: 10.1126/SCIENCE.1116304