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Fluorine in PDB 4ikt: 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-(5-(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-(5-(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-(5-(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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine, PDB code: 4ikt 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) 31.16 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.185, 77.372, 47.690, 90.00, 91.73, 90.00
R / Rfree (%) 19.3 / 22

Other elements in 4ikt:

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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine also contains other interesting chemical elements:

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

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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine (pdb code 4ikt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine, PDB code: 4ikt:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4ikt

Go back to Fluorine Binding Sites List in 4ikt
Fluorine binding site 1 out of 3 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-(5-(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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:45.1
occ:1.00
F3 A:TFV401 0.0 45.1 1.0
C18 A:TFV401 1.3 43.0 1.0
F2 A:TFV401 2.1 44.4 1.0
F1 A:TFV401 2.1 44.7 1.0
C15 A:TFV401 2.3 41.6 1.0
C16 A:TFV401 2.7 41.2 1.0
C A:THR311 3.1 25.6 1.0
O A:THR311 3.2 25.7 1.0
N A:ALA312 3.3 25.6 1.0
CA A:THR311 3.6 26.0 1.0
C14 A:TFV401 3.6 41.1 1.0
CA A:ALA312 3.8 25.4 1.0
N A:THR311 4.1 24.8 1.0
C17 A:TFV401 4.1 41.0 1.0
N A:ASN314 4.4 25.1 1.0
C A:PRO313 4.6 25.3 1.0
C A:HIS310 4.7 23.8 1.0
CA A:ASN314 4.7 25.4 1.0
N6 A:TFV401 4.7 40.0 1.0
CB A:ALA312 4.7 25.9 1.0
CB A:ASN314 4.8 25.5 1.0
O A:PRO313 4.9 25.0 1.0
C A:ALA312 4.9 25.1 1.0
O A:HIS310 5.0 23.8 1.0
C13 A:TFV401 5.0 40.5 1.0
CB A:THR311 5.0 26.3 1.0

Fluorine binding site 2 out of 3 in 4ikt

Go back to Fluorine Binding Sites List in 4ikt
Fluorine binding site 2 out of 3 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-(5-(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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.7
occ:1.00
F1 A:TFV401 0.0 44.7 1.0
C18 A:TFV401 1.3 43.0 1.0
F3 A:TFV401 2.1 45.1 1.0
F2 A:TFV401 2.2 44.4 1.0
C15 A:TFV401 2.3 41.6 1.0
C14 A:TFV401 2.9 41.1 1.0
OD1 A:ASN314 3.5 26.8 1.0
C16 A:TFV401 3.5 41.2 1.0
CB A:ASN314 3.6 25.5 1.0
CG A:ASN314 3.9 26.6 1.0
CA A:ASN314 4.0 25.4 1.0
O A:HOH592 4.1 30.1 1.0
N6 A:TFV401 4.2 40.0 1.0
N A:ASN314 4.3 25.1 1.0
C17 A:TFV401 4.6 41.0 1.0
O A:THR311 4.7 25.7 1.0
C13 A:TFV401 4.9 40.5 1.0

Fluorine binding site 3 out of 3 in 4ikt

Go back to Fluorine Binding Sites List in 4ikt
Fluorine binding site 3 out of 3 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-(5-(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-(5-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.4
occ:1.00
F2 A:TFV401 0.0 44.4 1.0
C18 A:TFV401 1.3 43.0 1.0
F3 A:TFV401 2.1 45.1 1.0
F1 A:TFV401 2.2 44.7 1.0
C15 A:TFV401 2.3 41.6 1.0
C14 A:TFV401 3.0 41.1 1.0
O A:THR311 3.1 25.7 1.0
C16 A:TFV401 3.3 41.2 1.0
O A:HOH592 3.4 30.1 1.0
CB A:HIS303 3.5 19.0 1.0
C A:THR311 3.7 25.6 1.0
N A:THR311 4.0 24.8 1.0
CA A:ASN314 4.0 25.4 1.0
O A:PRO313 4.0 25.0 1.0
CA A:HIS303 4.1 19.3 1.0
N A:ASN314 4.1 25.1 1.0
OD1 A:ASN314 4.2 26.8 1.0
CA A:THR311 4.2 26.0 1.0
N6 A:TFV401 4.3 40.0 1.0
C A:PRO313 4.3 25.3 1.0
CB A:ASN314 4.3 25.5 1.0
N A:ALA312 4.5 25.6 1.0
O A:GLY302 4.5 20.7 1.0
C17 A:TFV401 4.5 41.0 1.0
C A:HIS310 4.5 23.8 1.0
N A:GLY304 4.7 21.2 1.0
CB A:HIS310 4.7 22.7 1.0
CG A:ASN314 4.7 26.6 1.0
CG A:HIS303 4.8 18.3 1.0
CA A:ALA312 4.8 25.4 1.0
CL A:TFV401 4.9 30.3 1.0
C13 A:TFV401 4.9 40.5 1.0
C A:HIS303 4.9 20.3 1.0
CA A:HIS310 5.0 22.8 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: Sun Dec 13 12:04:39 2020

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