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Fluorine in PDB 6y9h: Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)

Enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2):
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h was solved by A.Sandner, A.Heine, G.Klebe, N.Abazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.333, 71.29, 72.534, 90, 100.5, 90
R / Rfree (%) 13.8 / 17

Other elements in 6y9h:

The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) (pdb code 6y9h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6y9h

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Fluorine binding site 1 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:21.9
occ:0.56
 F1 C:OGZ3 0.0 21.9 0.6
C20 C:OGZ3 1.4 23.6 0.6
F C:OGZ3 2.2 24.7 0.6
F2 C:OGZ3 2.2 26.4 0.6
C19 C:OGZ3 2.4 20.2 0.6
HG13 H:VAL213 2.6 15.6 1.0
C21 C:OGZ3 2.8 17.9 0.6
O H:TRP215 3.1 12.4 1.0
C16 C:OGZ3 3.2 35.3 0.4
C17 C:OGZ3 3.2 35.6 0.4
H H:PHE227 3.3 12.9 1.0
H H:TRP215 3.3 13.9 1.0
CG1 H:VAL213 3.5 13.0 1.0
H H:SER214 3.5 11.8 1.0
C H:TRP215 3.5 12.6 1.0
O H:PHE227 3.5 10.8 1.0
HG12 H:VAL213 3.6 15.6 1.0
HA3 H:GLY226 3.6 15.3 1.0
N H:TRP215 3.6 11.5 1.0
C18 C:OGZ3 3.7 19.4 0.6
HA2 H:GLY226 3.7 15.3 1.0
HB3 H:ALA190 3.7 22.0 1.0
N H:PHE227 3.9 10.8 1.0
HG11 H:VAL213 3.9 15.6 1.0
HB1 H:ALA190 3.9 22.0 1.0
CA H:TRP215 4.0 11.7 1.0
CA H:GLY226 4.0 12.7 1.0
N H:SER214 4.0 9.8 1.0
HA H:TRP215 4.1 14.0 1.0
HA H:VAL213 4.1 12.9 1.0
C15 C:OGZ3 4.2 17.5 0.6
HA3 H:GLY216 4.2 16.9 1.0
N H:GLY216 4.2 13.1 1.0
CB H:ALA190 4.3 18.3 1.0
C H:SER214 4.3 11.7 1.0
C H:GLY226 4.4 11.7 1.0
C15 C:OGZ3 4.4 35.4 0.4
C18 C:OGZ3 4.4 36.0 0.4
C H:PHE227 4.5 10.2 1.0
CA H:VAL213 4.6 10.7 1.0
CB H:VAL213 4.6 12.2 1.0
C H:VAL213 4.6 10.6 1.0
CA H:GLY216 4.7 14.1 1.0
CZ H:TYR228 4.7 10.9 1.0
H H:GLY216 4.7 15.8 1.0
CA H:PHE227 4.8 10.5 1.0
C17 C:OGZ3 4.8 19.6 0.6
CA H:SER214 4.8 10.1 1.0
OH H:TYR228 4.8 12.7 1.0
HG22 H:VAL213 4.8 16.0 1.0
OD1 H:ASP189 4.9 14.6 1.0
HH H:TYR228 4.9 15.2 1.0
HB2 H:ALA190 4.9 22.0 1.0
H H:ALA190 4.9 17.0 1.0
HA2 H:GLY216 4.9 16.9 1.0
CE2 H:TYR228 4.9 11.4 1.0
CE1 H:TYR228 5.0 11.0 1.0
C16 C:OGZ3 5.0 18.8 0.6

Fluorine binding site 2 out of 6 in 6y9h

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Fluorine binding site 2 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:36.9
occ:0.44
 F1 C:OGZ3 0.0 36.9 0.4
C20 C:OGZ3 1.3 36.7 0.4
OE2 H:GLU192 1.5 29.3 0.6
OE1 H:GLU192 1.7 30.0 0.6
CD H:GLU192 1.8 28.6 0.6
F C:OGZ3 2.1 37.0 0.4
F2 C:OGZ3 2.1 36.9 0.4
C19 C:OGZ3 2.4 36.0 0.4
C17 C:OGZ3 2.8 19.6 0.6
C21 C:OGZ3 3.2 35.6 0.4
C16 C:OGZ3 3.2 18.8 0.6
C18 C:OGZ3 3.2 36.0 0.4
CG H:GLU192 3.3 27.5 0.6
H H:GLU192 3.4 27.4 0.4
H H:GLU192 3.4 28.9 0.6
SG H:CYS220 3.5 21.8 1.0
HB2 H:GLU192 3.5 25.9 0.4
HG3 H:GLU192 3.6 33.0 0.6
HG2 H:GLU192 3.7 33.0 0.6
N H:GLU192 3.9 22.9 0.4
N H:GLU192 3.9 24.1 0.6
O H:GLY219 4.1 22.5 1.0
HA H:CYS191 4.1 24.9 1.0
C18 C:OGZ3 4.1 19.4 0.6
HB2 H:GLU192 4.1 31.1 0.6
H H:GLY219 4.2 23.6 1.0
HA2 H:GLY219 4.2 24.6 1.0
CB H:GLU192 4.2 25.9 0.6
C H:GLY219 4.3 21.1 1.0
CB H:GLU192 4.3 21.6 0.4
O C:HOH103 4.4 28.4 1.0
SG H:CYS191 4.4 21.4 1.0
C15 C:OGZ3 4.4 35.4 0.4
HA H:GLU192 4.4 26.1 0.4
C17 C:OGZ3 4.5 35.6 0.4
HG3 H:GLU146 4.5 36.1 1.0
CA H:GLU192 4.5 24.1 0.6
HA H:GLU192 4.5 29.0 0.6
CA H:GLU192 4.5 21.8 0.4
C15 C:OGZ3 4.5 17.5 0.6
CA H:GLY219 4.6 20.4 1.0
HB3 H:GLU192 4.6 25.9 0.4
N H:GLY219 4.7 19.6 1.0
C H:CYS191 4.7 22.9 1.0
CA H:CYS191 4.8 20.7 1.0
C16 C:OGZ3 4.9 35.3 0.4
N H:CYS220 4.9 19.3 1.0

Fluorine binding site 3 out of 6 in 6y9h

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Fluorine binding site 3 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:24.7
occ:0.56
 F C:OGZ3 0.0 24.7 0.6
C20 C:OGZ3 1.3 23.6 0.6
F2 C:OGZ3 2.0 26.4 0.6
F1 C:OGZ3 2.2 21.9 0.6
C19 C:OGZ3 2.3 20.2 0.6
HA2 H:GLY226 2.4 15.3 1.0
HA3 H:GLY216 2.7 16.9 1.0
HA3 H:GLY226 2.8 15.3 1.0
C18 C:OGZ3 2.8 19.4 0.6
C17 C:OGZ3 2.9 35.6 0.4
O H:HOH403 3.0 29.6 1.0
CA H:GLY226 3.0 12.7 1.0
O H:TRP215 3.2 12.4 1.0
H H:PHE227 3.4 12.9 1.0
OD1 H:ASP189 3.5 14.6 1.0
CA H:GLY216 3.5 14.1 1.0
C21 C:OGZ3 3.5 17.9 0.6
C18 C:OGZ3 3.6 36.0 0.4
C H:TRP215 3.6 12.6 1.0
C16 C:OGZ3 3.7 35.3 0.4
N H:GLY216 3.8 13.1 1.0
HA2 H:GLY216 3.8 16.9 1.0
N H:PHE227 3.9 10.8 1.0
C H:GLY226 4.0 11.7 1.0
N H:GLY226 4.1 13.0 1.0
OD2 H:ASP189 4.1 16.6 1.0
C17 C:OGZ3 4.1 19.6 0.6
HB3 H:ALA190 4.1 22.0 1.0
CG H:ASP189 4.2 15.7 1.0
H H:GLY216 4.3 15.8 1.0
H H:ALA190 4.4 17.0 1.0
O H:ALA190 4.4 16.0 1.0
HB1 H:ALA190 4.5 22.0 1.0
H H:GLY226 4.5 15.6 1.0
HG13 H:VAL213 4.5 15.6 1.0
O H:TYR225 4.5 14.0 1.0
H H:TRP215 4.7 13.9 1.0
O H:HOH455 4.7 14.5 1.0
C15 C:OGZ3 4.7 17.5 0.6
O H:HOH460 4.7 25.8 1.0
CB H:ALA190 4.7 18.3 1.0
C H:TYR225 4.7 12.6 1.0
CA H:TRP215 4.8 11.7 1.0
C H:GLY216 4.8 15.5 1.0
HA H:TRP215 4.8 14.0 1.0
C19 C:OGZ3 4.8 36.0 0.4
C H:ALA190 4.8 16.3 1.0
C15 C:OGZ3 4.9 35.4 0.4
C16 C:OGZ3 4.9 18.8 0.6
O H:GLY219 5.0 22.5 1.0
N H:TRP215 5.0 11.5 1.0
O H:PHE227 5.0 10.8 1.0
N H:ALA190 5.0 14.2 1.0

Fluorine binding site 4 out of 6 in 6y9h

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Fluorine binding site 4 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:37.0
occ:0.44
 F C:OGZ3 0.0 37.0 0.4
C20 C:OGZ3 1.3 36.7 0.4
F1 C:OGZ3 2.1 36.9 0.4
F2 C:OGZ3 2.1 36.9 0.4
O H:GLY219 2.3 22.5 1.0
C19 C:OGZ3 2.3 36.0 0.4
H H:GLY219 2.4 23.6 1.0
C17 C:OGZ3 2.6 19.6 0.6
C18 C:OGZ3 2.8 36.0 0.4
C H:GLY219 2.8 21.1 1.0
N H:GLY219 2.8 19.6 1.0
HA2 H:GLY219 3.0 24.6 1.0
CA H:GLY219 3.0 20.4 1.0
OE2 H:GLU192 3.2 29.3 0.6
C18 C:OGZ3 3.4 19.4 0.6
C16 C:OGZ3 3.5 18.8 0.6
C21 C:OGZ3 3.6 35.6 0.4
O H:GLY216 3.6 18.6 1.0
OE1 H:GLU192 3.7 30.0 0.6
SG H:CYS220 3.7 21.8 1.0
C H:GLU217 3.8 18.5 1.0
C H:GLY216 3.8 15.5 1.0
CD H:GLU192 3.8 28.6 0.6
N H:CYS220 3.8 19.3 1.0
HA H:GLU217 3.9 19.7 1.0
HA3 H:GLY219 4.0 24.6 1.0
N H:GLU217 4.1 14.9 1.0
C17 C:OGZ3 4.1 35.6 0.4
CA H:GLU217 4.2 16.4 1.0
HA3 H:GLY216 4.2 16.9 1.0
HA H:CYS220 4.3 23.3 1.0
H H:CYS220 4.4 23.2 1.0
CA H:GLY216 4.6 14.1 1.0
CA H:CYS220 4.6 19.4 1.0
H H:GLY216 4.6 15.8 1.0
H H:GLU217 4.6 17.9 1.0
N C:DPN1 4.6 15.1 0.6
HG3 H:GLU146 4.6 36.1 1.0
HA H:CYS191 4.6 24.9 1.0
O H:HOH403 4.7 29.6 1.0
O H:GLU217 4.7 22.6 1.0
C19 C:OGZ3 4.7 20.2 0.6
N C:DPN1 4.7 37.0 0.4
C15 C:OGZ3 4.7 35.4 0.4
C15 C:OGZ3 4.8 17.5 0.6
CB H:CYS220 4.9 21.4 1.0
O C:HOH103 4.9 28.4 1.0
N H:GLY216 4.9 13.1 1.0
C16 C:OGZ3 4.9 35.3 0.4

Fluorine binding site 5 out of 6 in 6y9h

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Fluorine binding site 5 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:26.4
occ:0.56
 F2 C:OGZ3 0.0 26.4 0.6
C20 C:OGZ3 1.3 23.6 0.6
F C:OGZ3 2.0 24.7 0.6
F1 C:OGZ3 2.2 21.9 0.6
HB3 H:ALA190 2.3 22.0 1.0
C19 C:OGZ3 2.3 20.2 0.6
HB1 H:ALA190 2.5 22.0 1.0
CB H:ALA190 2.7 18.3 1.0
C17 C:OGZ3 2.7 35.6 0.4
H H:ALA190 3.1 17.0 1.0
C18 C:OGZ3 3.1 19.4 0.6
C H:ALA190 3.2 16.3 1.0
OD1 H:ASP189 3.3 14.6 1.0
CA H:ALA190 3.3 15.4 1.0
C21 C:OGZ3 3.3 17.9 0.6
O H:ALA190 3.3 16.0 1.0
HG13 H:VAL213 3.3 15.6 1.0
C16 C:OGZ3 3.4 35.3 0.4
N H:ALA190 3.5 14.2 1.0
HB2 H:ALA190 3.6 22.0 1.0
HA3 H:GLY226 3.7 15.3 1.0
C18 C:OGZ3 3.8 36.0 0.4
HG11 H:VAL213 3.9 15.6 1.0
N H:CYS191 3.9 18.4 1.0
CG1 H:VAL213 4.0 13.0 1.0
CG H:ASP189 4.1 15.7 1.0
HA2 H:GLY226 4.1 15.3 1.0
HA H:ALA190 4.2 18.5 1.0
H H:CYS191 4.3 22.1 1.0
HA H:CYS191 4.3 24.9 1.0
O H:HOH403 4.3 29.6 1.0
C17 C:OGZ3 4.4 19.6 0.6
CA H:GLY226 4.4 12.7 1.0
HG12 H:VAL213 4.4 15.6 1.0
HH H:TYR228 4.4 15.2 1.0
OD2 H:ASP189 4.4 16.6 1.0
OH H:TYR228 4.5 12.7 1.0
C15 C:OGZ3 4.5 17.5 0.6
HA3 H:GLY216 4.5 16.9 1.0
O H:HOH455 4.6 14.5 1.0
CA H:CYS191 4.7 20.7 1.0
O H:TRP215 4.7 12.4 1.0
C15 C:OGZ3 4.7 35.4 0.4
C H:ASP189 4.7 14.6 1.0
H H:PHE227 4.8 12.9 1.0
C16 C:OGZ3 4.9 18.8 0.6

Fluorine binding site 6 out of 6 in 6y9h

Go back to Fluorine Binding Sites List in 6y9h
Fluorine binding site 6 out of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:36.9
occ:0.44
 F2 C:OGZ3 0.0 36.9 0.4
C20 C:OGZ3 1.3 36.7 0.4
OE2 H:GLU192 2.1 29.3 0.6
F C:OGZ3 2.1 37.0 0.4
F1 C:OGZ3 2.1 36.9 0.4
C19 C:OGZ3 2.4 36.0 0.4
O C:HOH103 2.8 28.4 1.0
C21 C:OGZ3 2.8 35.6 0.4
C17 C:OGZ3 3.0 19.6 0.6
C16 C:OGZ3 3.1 18.8 0.6
CD H:GLU192 3.1 28.6 0.6
N C:DPN1 3.2 15.1 0.6
N C:DPN1 3.3 37.0 0.4
H H:GLY219 3.4 23.6 1.0
O H:GLY216 3.5 18.6 1.0
C18 C:OGZ3 3.6 36.0 0.4
OE1 H:GLU192 3.7 30.0 0.6
O C:DPN1 3.9 12.9 0.6
O C:DPN1 3.9 36.9 0.4
O C:PRO2 4.0 15.1 0.6
O C:PRO2 4.1 36.5 0.4
N H:GLY219 4.2 19.6 1.0
C15 C:OGZ3 4.2 35.4 0.4
HG3 H:GLU192 4.2 33.0 0.6
C C:DPN1 4.3 12.9 0.6
C18 C:OGZ3 4.3 19.4 0.6
C C:DPN1 4.3 36.8 0.4
CG H:GLU192 4.3 27.5 0.6
H H:GLY216 4.3 15.8 1.0
C15 C:OGZ3 4.3 17.5 0.6
C H:GLY216 4.3 15.5 1.0
HA H:GLU217 4.3 19.7 1.0
CA C:DPN1 4.4 13.9 0.6
O H:GLY219 4.4 22.5 1.0
CA C:DPN1 4.4 36.8 0.4
HA2 H:GLY219 4.5 24.6 1.0
HG2 H:GLU192 4.6 33.0 0.6
C17 C:OGZ3 4.7 35.6 0.4
C C:PRO2 4.7 13.7 0.6
CA H:GLY219 4.7 20.4 1.0
C C:PRO2 4.8 36.1 0.4
C H:GLY219 4.9 21.1 1.0
C16 C:OGZ3 4.9 35.3 0.4
HB2 H:GLU192 4.9 25.9 0.4
CA H:GLU217 5.0 16.4 1.0
N H:GLU217 5.0 14.9 1.0
N H:GLY216 5.0 13.1 1.0

Reference:

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) To Be Published.
Page generated: Tue Jul 15 17:39:02 2025

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