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Fluorine in PDB 4iks: Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine

Enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine

All present enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine, PDB code: 4iks was solved by A.Addlagatta, C.Kishor, T.Arya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.219, 77.332, 47.153, 90.00, 92.36, 90.00
R / Rfree (%) 18.4 / 21.6

Other elements in 4iks:

The structure of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine (pdb code 4iks). 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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine, PDB code: 4iks:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4iks

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Fluorine binding site 1 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.4
occ:0.50
 F1 A:TFD401 0.0 33.4 0.5
C18 A:TFD401 1.3 31.7 0.5
F2 A:TFD401 2.2 31.4 0.5
F3 A:TFD401 2.2 30.1 0.5
C14 A:TFD401 2.3 31.0 0.5
C15 A:TFD401 2.6 31.4 0.5
CE1 A:TYR300 3.3 15.5 1.0
N6 A:TFD401 3.6 30.4 0.5
CD1 A:TYR300 3.8 14.4 1.0
C16 A:TFD401 4.0 30.5 0.5
C17 A:TFD401 4.1 35.4 0.5
CZ A:TYR300 4.2 14.2 1.0
OH A:TYR300 4.4 14.1 1.0
C16 A:TFD401 4.4 35.5 0.5
O A:SER299 4.5 17.6 1.0
C13 A:TFD401 4.7 29.4 0.5
C11 A:TFD401 4.8 30.0 0.5
C17 A:TFD401 4.9 30.4 0.5
O A:HOH559 4.9 24.1 1.0
CG A:TYR300 4.9 16.0 1.0
O A:HOH523 4.9 12.1 1.0
CL A:TFD401 5.0 18.3 0.5
O A:HOH573 5.0 22.2 1.0

Fluorine binding site 2 out of 6 in 4iks

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Fluorine binding site 2 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.5
occ:0.50
 F1 A:TFD401 0.0 39.5 0.5
C18 A:TFD401 1.3 38.7 0.5
F2 A:TFD401 2.1 39.2 0.5
F3 A:TFD401 2.2 39.6 0.5
C14 A:TFD401 2.3 37.4 0.5
N6 A:TFD401 3.1 36.0 0.5
C15 A:TFD401 3.1 36.9 0.5
C13 A:TFD401 4.3 34.3 0.5
C16 A:TFD401 4.4 35.5 0.5
O A:HOH617 4.8 34.8 1.0
C17 A:TFD401 4.8 35.4 0.5

Fluorine binding site 3 out of 6 in 4iks

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Fluorine binding site 3 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:31.4
occ:0.50
 F2 A:TFD401 0.0 31.4 0.5
C18 A:TFD401 1.3 31.7 0.5
F3 A:TFD401 2.1 30.1 0.5
F1 A:TFD401 2.2 33.4 0.5
C14 A:TFD401 2.3 31.0 0.5
C17 A:TFD401 2.3 35.4 0.5
C16 A:TFD401 2.4 35.5 0.5
N6 A:TFD401 2.9 30.4 0.5
O A:HOH573 3.2 22.2 1.0
C15 A:TFD401 3.4 31.4 0.5
C13 A:TFD401 3.7 34.3 0.5
O A:HOH523 3.8 12.1 1.0
C15 A:TFD401 3.8 36.9 0.5
CE1 A:TYR300 4.1 15.5 1.0
C11 A:TFD401 4.1 30.0 0.5
C13 A:TFD401 4.2 29.4 0.5
N5 A:TFD401 4.4 32.8 0.5
OH A:TYR300 4.4 14.1 1.0
C16 A:TFD401 4.5 30.5 0.5
CZ3 A:TRP353 4.6 18.6 1.0
N6 A:TFD401 4.7 36.0 0.5
C14 A:TFD401 4.7 37.4 0.5
CZ A:TYR300 4.7 14.2 1.0
ND1 A:HIS212 4.8 13.2 1.0
CE1 A:HIS212 4.8 14.2 1.0
C17 A:TFD401 4.9 30.4 0.5
CD1 A:TYR300 5.0 14.4 1.0

Fluorine binding site 4 out of 6 in 4iks

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Fluorine binding site 4 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.2
occ:0.50
 F2 A:TFD401 0.0 39.2 0.5
C18 A:TFD401 1.3 38.7 0.5
F1 A:TFD401 2.1 39.5 0.5
F3 A:TFD401 2.2 39.6 0.5
C14 A:TFD401 2.3 37.4 0.5
N6 A:TFD401 2.7 36.0 0.5
O A:TYR196 3.4 15.8 1.0
CB A:TYR196 3.5 17.8 1.0
C15 A:TFD401 3.6 36.9 0.5
O A:HOH617 3.6 34.8 1.0
CZ2 A:TRP353 3.9 17.3 1.0
C13 A:TFD401 4.0 34.3 0.5
C A:TYR196 4.2 16.5 1.0
CG A:TYR196 4.3 20.4 1.0
CD2 A:TYR196 4.3 22.5 1.0
CH2 A:TRP353 4.3 18.4 1.0
CA A:TYR196 4.3 17.5 1.0
CE2 A:TRP353 4.7 16.0 1.0
C16 A:TFD401 4.7 35.5 0.5
N5 A:TFD401 4.8 32.8 0.5
C17 A:TFD401 4.9 35.4 0.5

Fluorine binding site 5 out of 6 in 4iks

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Fluorine binding site 5 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.1
occ:0.50
 F3 A:TFD401 0.0 30.1 0.5
C18 A:TFD401 1.3 31.7 0.5
F2 A:TFD401 2.1 31.4 0.5
F1 A:TFD401 2.2 33.4 0.5
C14 A:TFD401 2.3 31.0 0.5
N6 A:TFD401 2.9 30.4 0.5
C8 A:TFD401 3.4 16.2 0.5
C17 A:TFD401 3.4 35.4 0.5
C15 A:TFD401 3.4 31.4 0.5
C7 A:TFD401 3.5 15.8 0.5
C11 A:TFD401 3.5 30.0 0.5
CE1 A:HIS212 3.6 14.2 1.0
CE1 A:TYR300 3.7 15.5 1.0
C7 A:TFD401 3.8 23.6 0.5
C9 A:TFD401 3.8 15.6 0.5
C8 A:TFD401 3.8 23.4 0.5
N3 A:TFD401 3.8 13.3 0.5
N4 A:TFD401 3.8 17.9 0.5
CL A:TFD401 4.0 18.3 0.5
N3 A:TFD401 4.0 22.8 0.5
C9 A:TFD401 4.0 23.1 0.5
CD1 A:TYR300 4.1 14.4 1.0
ND1 A:HIS212 4.1 13.2 1.0
C16 A:TFD401 4.1 35.5 0.5
N2 A:TFD401 4.2 9.4 0.5
C6 A:TFD401 4.2 12.4 0.5
C6 A:TFD401 4.2 21.2 0.5
C13 A:TFD401 4.2 29.4 0.5
N2 A:TFD401 4.2 20.4 0.5
N4 A:TFD401 4.2 26.5 0.5
C13 A:TFD401 4.4 34.3 0.5
N5 A:TFD401 4.4 32.8 0.5
C10 A:TFD401 4.5 28.8 0.5
O A:HOH523 4.5 12.1 1.0
CL A:TFD401 4.5 21.9 0.5
C12 A:TFD401 4.5 15.8 0.5
C16 A:TFD401 4.6 30.5 0.5
NE2 A:HIS212 4.8 12.2 1.0
C12 A:TFD401 4.8 23.3 0.5
CZ3 A:TRP353 4.9 18.6 1.0
C10 A:TFD401 4.9 20.9 0.5
CZ A:TYR300 4.9 14.2 1.0
C17 A:TFD401 4.9 30.4 0.5
O A:HOH573 5.0 22.2 1.0

Fluorine binding site 6 out of 6 in 4iks

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Fluorine binding site 6 out of 6 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with N1-(5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)-N2-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.6
occ:0.50
 F3 A:TFD401 0.0 39.6 0.5
C18 A:TFD401 1.3 38.7 0.5
F2 A:TFD401 2.2 39.2 0.5
F1 A:TFD401 2.2 39.5 0.5
C14 A:TFD401 2.3 37.4 0.5
C15 A:TFD401 2.7 36.9 0.5
N6 A:TFD401 3.5 36.0 0.5
O A:GLY352 4.0 15.2 1.0
C16 A:TFD401 4.1 35.5 0.5
CZ2 A:TRP353 4.2 17.3 1.0
CE2 A:TRP353 4.3 16.0 1.0
NE1 A:TRP353 4.5 14.9 1.0
O A:TYR196 4.6 15.8 1.0
C13 A:TFD401 4.6 34.3 0.5
CH2 A:TRP353 4.7 18.4 1.0
C A:GLY352 4.8 14.0 1.0
C17 A:TFD401 4.9 35.4 0.5
CD2 A:TRP353 4.9 12.8 1.0

Reference:

C.Kishor, T.Arya, R.Reddi, X.Chen, V.Saddanapu, A.K.Marapaka, R.Gumpena, D.Ma, J.O.Liu, A.Addlagatta. Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors Against Type I Methionine Aminopeptidases J.Med.Chem. V. 56 5295 2013.
ISSN: ISSN 0022-2623
PubMed: 23767698
DOI: 10.1021/JM400395P
Page generated: Thu Aug 1 02:31:48 2024

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