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Chlorine 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:

Fluorine (F) 6 atoms
Cobalt (Co) 3 atoms
Potassium (K) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4iks

Go back to Chlorine Binding Sites List in 4iks
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl401

b:18.3
occ:0.50
 CL A:TFD401 0.0 18.3 0.5
CL A:TFD401 1.0 21.9 0.5
C8 A:TFD401 1.8 16.2 0.5
C8 A:TFD401 1.8 23.4 0.5
N4 A:TFD401 2.2 26.5 0.5
C7 A:TFD401 2.3 23.6 0.5
C7 A:TFD401 2.7 15.8 0.5
C9 A:TFD401 2.8 15.6 0.5
N4 A:TFD401 2.9 17.9 0.5
C9 A:TFD401 3.1 23.1 0.5
C12 A:TFD401 3.2 15.8 0.5
C10 A:TFD401 3.5 28.8 0.5
N3 A:TFD401 3.6 22.8 0.5
C12 A:TFD401 3.7 23.3 0.5
O A:HOH583 3.8 26.6 1.0
C11 A:TFD401 3.9 30.0 0.5
O A:HOH559 3.9 24.1 1.0
N3 A:TFD401 4.0 13.3 0.5
F3 A:TFD401 4.0 30.1 0.5
N2 A:TFD401 4.0 9.4 0.5
CG A:HIS310 4.1 16.6 1.0
N2 A:TFD401 4.1 20.4 0.5
C14 A:TFD401 4.2 31.0 0.5
CD2 A:HIS310 4.2 17.0 1.0
C10 A:TFD401 4.3 20.9 0.5
N6 A:TFD401 4.3 30.4 0.5
CB A:HIS310 4.3 17.0 1.0
C6 A:TFD401 4.3 21.2 0.5
C15 A:TFD401 4.4 31.4 0.5
C6 A:TFD401 4.5 12.4 0.5
C13 A:TFD401 4.6 29.4 0.5
ND1 A:HIS310 4.6 16.6 1.0
C18 A:TFD401 4.6 31.7 0.5
C16 A:TFD401 4.7 30.5 0.5
NE2 A:HIS310 4.7 15.8 1.0
C17 A:TFD401 4.8 30.4 0.5
C11 A:TFD401 4.9 24.5 0.5
CE1 A:HIS310 4.9 16.6 1.0
F1 A:TFD401 5.0 33.4 0.5

Chlorine binding site 2 out of 2 in 4iks

Go back to Chlorine Binding Sites List in 4iks
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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:Cl401

b:21.9
occ:0.50
 CL A:TFD401 0.0 21.9 0.5
CL A:TFD401 1.0 18.3 0.5
C8 A:TFD401 1.8 23.4 0.5
C8 A:TFD401 2.1 16.2 0.5
C12 A:TFD401 2.5 15.8 0.5
C9 A:TFD401 2.6 15.6 0.5
C7 A:TFD401 2.7 23.6 0.5
C9 A:TFD401 2.8 23.1 0.5
O A:HOH583 2.8 26.6 1.0
N4 A:TFD401 3.0 26.5 0.5
C12 A:TFD401 3.1 23.3 0.5
C7 A:TFD401 3.3 15.8 0.5
O A:HOH559 3.4 24.1 1.0
CD2 A:HIS310 3.6 17.0 1.0
N4 A:TFD401 3.8 17.9 0.5
CG A:HIS310 3.8 16.6 1.0
N2 A:TFD401 4.0 9.4 0.5
N3 A:TFD401 4.0 22.8 0.5
N2 A:TFD401 4.0 20.4 0.5
CB A:HIS310 4.0 17.0 1.0
NE2 A:HIS310 4.3 15.8 1.0
C10 A:TFD401 4.4 28.8 0.5
N3 A:TFD401 4.4 13.3 0.5
C6 A:TFD401 4.5 21.2 0.5
ND1 A:HIS310 4.5 16.6 1.0
F3 A:TFD401 4.5 30.1 0.5
C6 A:TFD401 4.7 12.4 0.5
CE1 A:HIS310 4.7 16.6 1.0
C11 A:TFD401 4.8 30.0 0.5

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 Jul 21 16:49:21 2024

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