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Fluorine in PDB 4j8w: X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II)

Protein crystallography data

The structure of X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II), PDB code: 4j8w was solved by Z.Adhireksan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.96 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.780, 109.730, 181.910, 90.00, 90.00, 90.00
R / Rfree (%) 26.5 / 27.5

Other elements in 4j8w:

The structure of X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Osmium (Os) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II) (pdb code 4j8w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II), PDB code: 4j8w:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4j8w

Go back to Fluorine Binding Sites List in 4j8w
Fluorine binding site 1 out of 3 in the X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1102

b:0.2
occ:1.00
F1 D:1MK1102 0.0 0.2 1.0
C10 D:1MK1102 1.4 0.8 1.0
C9 D:1MK1102 2.3 0.7 1.0
C11 D:1MK1102 2.4 0.8 1.0
CB B:MET84 3.2 43.7 1.0
CG B:MET84 3.4 45.6 1.0
OH B:TYR88 3.6 50.5 1.0
C8 D:1MK1102 3.6 0.5 1.0
CE1 B:TYR88 3.6 47.0 1.0
C12 D:1MK1102 3.7 0.4 1.0
CZ B:TYR88 4.0 48.8 1.0
O D:TYR80 4.1 58.3 1.0
C7 D:1MK1102 4.1 0.2 1.0
CA B:MET84 4.7 43.5 1.0
CD1 B:TYR88 4.7 45.7 1.0
CE B:MET84 4.8 51.0 1.0
SD B:MET84 4.9 51.4 1.0

Fluorine binding site 2 out of 3 in 4j8w

Go back to Fluorine Binding Sites List in 4j8w
Fluorine binding site 2 out of 3 in the X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F203

b:0.8
occ:1.00
F1 H:1MK203 0.0 0.8 1.0
C10 H:1MK203 1.4 0.3 1.0
C9 H:1MK203 2.4 0.1 1.0
C11 H:1MK203 2.4 0.2 1.0
OE1 G:GLU92 2.6 54.6 1.0
CD1 H:LEU103 3.2 50.0 1.0
CD G:GLU92 3.6 52.5 1.0
C8 H:1MK203 3.6 0.8 1.0
C12 H:1MK203 3.7 0.9 1.0
CB G:GLU92 3.7 46.2 1.0
CG H:LEU103 3.9 51.2 1.0
N H:LEU103 4.0 50.7 1.0
OE2 G:GLU61 4.0 57.2 1.0
CB H:LEU103 4.1 50.7 1.0
CD2 H:LEU103 4.1 50.6 1.0
C7 H:1MK203 4.1 0.7 1.0
CA H:LEU103 4.1 50.8 1.0
CG G:GLU92 4.1 48.4 1.0
CB H:GLU102 4.3 51.4 1.0
OD2 G:ASP90 4.4 49.9 1.0
C H:GLU102 4.5 50.8 1.0
OE2 G:GLU92 4.6 54.5 1.0
CD G:GLU61 4.8 54.9 1.0
OD1 G:ASP90 4.9 52.5 1.0

Fluorine binding site 3 out of 3 in 4j8w

Go back to Fluorine Binding Sites List in 4j8w
Fluorine binding site 3 out of 3 in the X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of NCP145 with Chlorido(Eta-6-P-Cymene)(N- Fluorophenyl-2-Pyridinecarbothioamide)Osmium(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F204

b:0.9
occ:1.00
F1 H:1MK204 0.0 0.9 1.0
C10 H:1MK204 1.4 0.8 1.0
C9 H:1MK204 2.3 0.6 1.0
C11 H:1MK204 2.4 0.6 1.0
CG F:MET84 3.4 40.4 1.0
C8 H:1MK204 3.6 0.4 1.0
C12 H:1MK204 3.7 0.6 1.0
C7 H:1MK204 4.1 0.2 1.0
SD F:MET84 4.2 45.8 1.0
CB F:MET84 4.7 37.6 1.0
CE F:MET84 5.0 45.4 1.0

Reference:

S.M.Meier, M.Hanif, Z.Adhireksan, V.Pichler, M.Novak, E.Jirkovsky, M.A.Jakupec, V.B.Arion, C.A.Davey, B.K.Keppler, C.G.Hartinger. Novel Metal(II) Arene 2-Pyridinecarbothioamides: A Rationale to Orally Active Organometallic Anticancer Agents Chem Sci V. 4 1837 2013.
ISSN: ISSN 2041-6520
DOI: 10.1039/C3SC22294B
Page generated: Sun Dec 13 12:05:17 2020

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