Fluorine in PDB 3opd: Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative

The structure of Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative, PDB code: 3opd was solved by J.C.Pizarro, A.K.Wernimont, A.Hutchinson, H.Sullivan, K.Chamberlain, J.Weadge, D.Cossar, Y.Li, I.Kozieradzki, A.Bochkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, P.G.Wyatt, A.H.Fairlamb, C.Mackenzie, M.A.J.Ferguson, R.Hui, T.Hills, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.915, 72.103, 152.147, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.7

The binding sites of Fluorine atom in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative (pdb code 3opd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative, PDB code: 3opd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F214 b:46.3 occ:1.00 F1 A:HIE214 0.0 46.3 1.0 C23 A:HIE214 1.3 45.2 1.0 F3 A:HIE214 2.0 45.8 1.0 C14 A:HIE214 2.3 43.1 1.0 F2 A:HIE214 2.3 45.8 1.0 C15 A:HIE214 3.1 40.2 1.0 O1 A:HIE214 3.1 41.8 1.0 N4 A:HIE214 3.3 46.2 1.0 CB A:ALA96 3.3 42.5 1.0 CD1 A:ILE95 3.4 57.8 1.0 C20 A:HIE214 3.5 39.2 1.0 CA A:ALA96 3.5 41.5 1.0 CB A:LEU92 3.5 50.6 1.0 CD1 A:LEU92 3.6 53.9 1.0 O A:ASN91 3.6 56.0 1.0 N A:ALA96 3.7 42.4 1.0 CG1 A:ILE95 4.0 44.4 1.0 CG A:LEU92 4.0 54.3 1.0 N3 A:HIE214 4.2 45.4 1.0 C16 A:HIE214 4.3 40.8 1.0 C A:ILE95 4.3 46.7 1.0 C A:ASN91 4.5 55.7 1.0 CA A:LEU92 4.6 52.1 1.0 O A:ILE95 4.8 46.8 1.0 O A:GLY120 4.8 36.6 1.0 N A:LEU92 4.9 52.6 1.0 C19 A:HIE214 4.9 36.0 1.0

Fluorine binding site 2 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F214 b:45.8 occ:1.00 F2 A:HIE214 0.0 45.8 1.0 C23 A:HIE214 1.4 45.2 1.0 F1 A:HIE214 2.3 46.3 1.0 C14 A:HIE214 2.3 43.1 1.0 F3 A:HIE214 2.3 45.8 1.0 O1 A:HIE214 3.0 41.8 1.0 C15 A:HIE214 3.1 40.2 1.0 CE1 A:TYR124 3.3 39.9 1.0 N4 A:HIE214 3.4 46.2 1.0 C20 A:HIE214 3.5 39.2 1.0 CD1 A:TYR124 3.7 38.3 1.0 CG1 A:VAL121 3.8 39.8 1.0 O A:HOH248 4.0 40.2 1.0 CB A:ALA96 4.0 42.5 1.0 CA A:VAL121 4.0 35.9 1.0 CA A:ALA96 4.1 41.5 1.0 O A:GLY120 4.2 36.6 1.0 CB A:VAL121 4.2 39.5 1.0 N3 A:HIE214 4.3 45.4 1.0 C16 A:HIE214 4.3 40.8 1.0 CZ A:TYR124 4.4 44.9 1.0 C A:VAL121 4.7 38.8 1.0 O A:VAL121 4.7 40.0 1.0 CB A:PHE123 4.7 29.3 1.0 OH A:TYR124 4.7 45.0 1.0 CD2 A:PHE123 4.8 32.7 1.0 N A:ALA96 4.9 42.4 1.0 C19 A:HIE214 4.9 36.0 1.0 N A:VAL121 4.9 36.2 1.0 C A:GLY120 5.0 36.8 1.0

Fluorine binding site 3 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F214 b:45.8 occ:1.00 F3 A:HIE214 0.0 45.8 1.0 C23 A:HIE214 1.3 45.2 1.0 F1 A:HIE214 2.0 46.3 1.0 F2 A:HIE214 2.3 45.8 1.0 C14 A:HIE214 2.4 43.1 1.0 N4 A:HIE214 2.7 46.2 1.0 O A:GLY120 2.9 36.6 1.0 CD1 A:ILE95 3.0 57.8 1.0 O A:HOH248 3.6 40.2 1.0 C15 A:HIE214 3.8 40.2 1.0 C A:GLY120 4.0 36.8 1.0 N3 A:HIE214 4.0 45.4 1.0 CD1 A:LEU92 4.1 53.9 1.0 CG1 A:ILE95 4.2 44.4 1.0 CG1 A:VAL121 4.3 39.8 1.0 CA A:VAL121 4.3 35.9 1.0 CA A:ALA96 4.4 41.5 1.0 N A:ALA96 4.5 42.4 1.0 O1 A:HIE214 4.5 41.8 1.0 N A:VAL121 4.6 36.2 1.0 C16 A:HIE214 4.6 40.8 1.0 C A:ILE95 4.6 46.7 1.0 C20 A:HIE214 4.7 39.2 1.0 O A:ILE95 4.7 46.8 1.0 CB A:ALA96 4.7 42.5 1.0 CB A:LEU92 4.8 50.6 1.0 CB A:VAL121 4.9 39.5 1.0

Fluorine binding site 4 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F214 b:61.2 occ:1.00 F1 B:HIE214 0.0 61.2 1.0 C23 B:HIE214 1.3 57.8 1.0 F3 B:HIE214 2.0 58.0 1.0 F2 B:HIE214 2.2 59.2 1.0 C14 B:HIE214 2.2 51.6 1.0 O1 B:HIE214 2.9 54.0 1.0 CB B:ALA96 2.9 60.5 1.0 C15 B:HIE214 3.0 47.9 1.0 N4 B:HIE214 3.3 50.8 1.0 C20 B:HIE214 3.3 50.0 1.0 O B:ASN91 3.5 62.2 1.0 CB B:LEU92 3.8 56.0 1.0 CD1 B:LEU92 3.9 56.3 1.0 CA B:ALA96 4.0 60.0 1.0 CG B:LEU92 4.2 58.6 1.0 O B:HOH283 4.2 66.5 1.0 C B:ASN91 4.2 62.7 1.0 C16 B:HIE214 4.3 46.5 1.0 N3 B:HIE214 4.3 48.6 1.0 CE1 B:TYR124 4.3 44.7 1.0 CG1 B:VAL121 4.7 55.6 1.0 N B:ALA96 4.7 62.2 1.0 O B:GLY120 4.8 54.7 1.0 N B:LEU92 4.8 59.5 1.0 CA B:LEU92 4.8 58.5 1.0 C19 B:HIE214 4.8 45.6 1.0

Fluorine binding site 5 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F214 b:59.2 occ:1.00 F2 B:HIE214 0.0 59.2 1.0 C23 B:HIE214 1.4 57.8 1.0 F1 B:HIE214 2.2 61.2 1.0 F3 B:HIE214 2.3 58.0 1.0 C14 B:HIE214 2.3 51.6 1.0 CE1 B:TYR124 3.0 44.7 1.0 C15 B:HIE214 3.2 47.9 1.0 O1 B:HIE214 3.2 54.0 1.0 CD1 B:TYR124 3.3 43.8 1.0 N4 B:HIE214 3.3 50.8 1.0 C20 B:HIE214 3.6 50.0 1.0 CA B:VAL121 3.7 49.0 1.0 CG1 B:VAL121 3.9 55.6 1.0 O B:HOH221 4.0 45.6 1.0 CB B:VAL121 4.0 54.2 1.0 O B:VAL121 4.1 51.0 1.0 C B:VAL121 4.2 50.3 1.0 CZ B:TYR124 4.2 49.1 1.0 CB B:PHE123 4.2 39.4 1.0 O B:GLY120 4.3 54.7 1.0 CB B:ALA96 4.3 60.5 1.0 N3 B:HIE214 4.3 48.6 1.0 CD2 B:PHE123 4.4 43.3 1.0 C16 B:HIE214 4.4 46.5 1.0 CG B:TYR124 4.5 42.0 1.0 OH B:TYR124 4.7 46.8 1.0 CG B:PHE123 4.8 41.0 1.0 N B:VAL121 4.8 49.1 1.0 N B:PHE123 4.9 38.1 1.0 N B:TYR124 4.9 39.3 1.0 C B:GLY120 5.0 52.7 1.0

Fluorine binding site 6 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


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 N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F214 b:58.0 occ:1.00 F3 B:HIE214 0.0 58.0 1.0 C23 B:HIE214 1.3 57.8 1.0 F1 B:HIE214 2.0 61.2 1.0 C14 B:HIE214 2.3 51.6 1.0 F2 B:HIE214 2.3 59.2 1.0 N4 B:HIE214 2.6 50.8 1.0 O B:GLY120 2.8 54.7 1.0 O B:HOH283 3.1 66.5 1.0 O B:HOH221 3.2 45.6 1.0 C15 B:HIE214 3.7 47.9 1.0 CD1 B:LEU92 3.9 56.3 1.0 O B:HOH240 3.9 59.6 1.0 C B:GLY120 3.9 52.7 1.0 N3 B:HIE214 4.0 48.6 1.0 CA B:VAL121 4.0 49.0 1.0 CB B:ALA96 4.2 60.5 1.0 CG1 B:VAL121 4.2 55.6 1.0 N B:VAL121 4.4 49.1 1.0 O1 B:HIE214 4.5 54.0 1.0 C16 B:HIE214 4.6 46.5 1.0 CA B:ALA96 4.6 60.0 1.0 C20 B:HIE214 4.7 50.0 1.0 CB B:LEU92 4.7 56.0 1.0 CB B:VAL121 4.7 54.2 1.0 CG B:LEU92 4.8 58.6 1.0 C B:VAL121 4.8 50.3 1.0 C3 B:HIE214 5.0 49.8 1.0

Fluorine binding site 7 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:F214 b:58.1 occ:1.00 F1 C:HIE214 0.0 58.1 1.0 C23 C:HIE214 1.4 58.6 1.0 F3 C:HIE214 2.2 58.1 1.0 F2 C:HIE214 2.2 59.8 1.0 C14 C:HIE214 2.3 58.6 1.0 O1 C:HIE214 2.9 53.1 1.0 CB C:ALA96 2.9 66.8 1.0 C15 C:HIE214 3.0 55.7 1.0 C20 C:HIE214 3.3 53.2 1.0 O C:ASN91 3.4 57.9 1.0 N4 C:HIE214 3.4 61.1 1.0 CB C:LEU92 3.7 60.1 1.0 CD1 C:LEU92 3.7 62.0 1.0 CG C:LEU92 4.0 63.3 1.0 C C:ASN91 4.1 60.2 1.0 CA C:ALA96 4.2 66.6 1.0 C16 C:HIE214 4.2 56.2 1.0 N3 C:HIE214 4.3 60.2 1.0 O C:HOH266 4.4 50.2 1.0 CE1 C:TYR124 4.6 45.4 1.0 N C:LEU92 4.6 60.9 1.0 CA C:LEU92 4.7 62.0 1.0 C19 C:HIE214 4.8 49.4 1.0 CG1 C:VAL121 4.8 45.8 1.0 O C:GLY120 4.9 52.5 1.0 CA C:ASN91 5.0 54.4 1.0

Fluorine binding site 8 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:F214 b:59.8 occ:1.00 F2 C:HIE214 0.0 59.8 1.0 C23 C:HIE214 1.3 58.6 1.0 F3 C:HIE214 2.2 58.1 1.0 F1 C:HIE214 2.2 58.1 1.0 C14 C:HIE214 2.3 58.6 1.0 C15 C:HIE214 3.2 55.7 1.0 CE1 C:TYR124 3.2 45.4 1.0 O1 C:HIE214 3.3 53.1 1.0 N4 C:HIE214 3.3 61.1 1.0 CD1 C:TYR124 3.5 44.8 1.0 C20 C:HIE214 3.6 53.2 1.0 CG1 C:VAL121 3.6 45.8 1.0 CA C:VAL121 3.7 41.8 1.0 CB C:VAL121 3.9 44.8 1.0 O C:GLY120 4.1 52.5 1.0 O C:VAL121 4.3 41.9 1.0 C C:VAL121 4.3 44.6 1.0 CB C:ALA96 4.3 66.8 1.0 N3 C:HIE214 4.4 60.2 1.0 CZ C:TYR124 4.4 54.6 1.0 C16 C:HIE214 4.4 56.2 1.0 CB C:PHE123 4.4 43.2 1.0 CD2 C:PHE123 4.6 43.0 1.0 N C:VAL121 4.7 43.9 1.0 OH C:TYR124 4.8 53.0 1.0 CG C:TYR124 4.8 42.6 1.0 C C:GLY120 4.9 50.6 1.0

Fluorine binding site 9 out of 9 in the Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the N-Terminal Domain of An HSP90 From Trypanosoma Brucei, TB10.26.1080 in the Presence of A Benzamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:F214 b:58.1 occ:1.00 F3 C:HIE214 0.0 58.1 1.0 C23 C:HIE214 1.3 58.6 1.0 F1 C:HIE214 2.2 58.1 1.0 F2 C:HIE214 2.2 59.8 1.0 C14 C:HIE214 2.3 58.6 1.0 N4 C:HIE214 2.6 61.1 1.0 O C:GLY120 2.8 52.5 1.0 O C:HOH266 3.5 50.2 1.0 C15 C:HIE214 3.7 55.7 1.0 CD1 C:LEU92 3.9 62.0 1.0 C C:GLY120 3.9 50.6 1.0 CB C:ALA96 3.9 66.8 1.0 N3 C:HIE214 4.0 60.2 1.0 CA C:VAL121 4.1 41.8 1.0 CG1 C:VAL121 4.2 45.8 1.0 N C:VAL121 4.4 43.9 1.0 C16 C:HIE214 4.5 56.2 1.0 O1 C:HIE214 4.6 53.1 1.0 C20 C:HIE214 4.6 53.2 1.0 CA C:ALA96 4.7 66.6 1.0 CB C:VAL121 4.7 44.8 1.0 CB C:LEU92 4.8 60.1 1.0 CG C:LEU92 4.8 63.3 1.0 C C:VAL121 4.9 44.6 1.0 C3 C:HIE214 5.0 63.1 1.0

J.C.Pizarro, T.Hills, G.Senisterra, A.K.Wernimont, C.Mackenzie, N.R.Norcross, M.A.Ferguson, P.G.Wyatt, I.H.Gilbert, R.Hui. Exploring the Trypanosoma Brucei HSP83 Potential As A Target For Structure Guided Drug Design. Plos Negl Trop Dis V. 7 E2492 2013.
ISSN: ESSN 1935-2735
PubMed: 24147171
DOI: 10.1371/JOURNAL.PNTD.0002492