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Cobalt 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:

Fluorine (F) 3 atoms
Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 3 binding sites of Cobalt 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 Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4ikt

Go back to Cobalt Binding Sites List in 4ikt
Cobalt 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 Cobalt with other atoms in the Co 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:Co402

b:16.2
occ:1.00
 O A:HOH580 1.8 16.2 1.0
OE2 A:GLU367 1.9 15.4 1.0
OD2 A:ASP240 2.1 12.4 1.0
NE2 A:HIS303 2.1 15.2 1.0
OE1 A:GLU336 2.3 16.3 1.0
CD A:GLU367 2.9 12.5 1.0
CG A:ASP240 3.0 15.2 1.0
CE1 A:HIS303 3.1 17.5 1.0
CO A:CO403 3.1 13.9 1.0
CD2 A:HIS303 3.1 18.3 1.0
CD A:GLU336 3.1 16.4 1.0
OE1 A:GLU367 3.2 16.3 1.0
OD1 A:ASP240 3.3 13.2 1.0
OE2 A:GLU336 3.4 17.5 1.0
OG1 A:THR334 3.6 16.9 1.0
O A:HOH579 3.8 18.3 1.0
CG2 A:THR334 3.9 16.0 1.0
CB A:THR334 4.1 16.7 1.0
ND1 A:HIS303 4.2 16.8 1.0
CB A:ASP240 4.2 14.7 1.0
CG A:HIS303 4.2 18.3 1.0
CG A:GLU367 4.2 14.2 1.0
O A:HOH517 4.3 13.7 1.0
CG A:GLU336 4.4 15.5 1.0
NE2 A:HIS310 4.8 18.1 1.0
O A:HOH578 4.8 18.1 1.0
CB A:GLU336 4.9 13.2 1.0
OD2 A:ASP229 4.9 17.6 1.0
CD2 A:HIS310 4.9 21.1 1.0
C12 A:TFV401 5.0 22.6 1.0

Cobalt binding site 2 out of 3 in 4ikt

Go back to Cobalt Binding Sites List in 4ikt
Cobalt 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 Cobalt with other atoms in the Co 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:Co403

b:13.9
occ:1.00
 O A:HOH580 2.1 16.2 1.0
OD1 A:ASP240 2.1 13.2 1.0
OE1 A:GLU367 2.1 16.3 1.0
OD1 A:ASP229 2.2 11.5 1.0
O A:HOH517 2.3 13.7 1.0
OD2 A:ASP229 2.4 17.6 1.0
CG A:ASP229 2.6 16.7 1.0
CG A:ASP240 3.0 15.2 1.0
CD A:GLU367 3.0 12.5 1.0
CO A:CO402 3.1 16.2 1.0
OD2 A:ASP240 3.2 12.4 1.0
OE2 A:GLU367 3.2 15.4 1.0
O A:HOH579 3.8 18.3 1.0
OG1 A:THR231 4.0 15.2 1.0
CB A:ASP229 4.1 13.7 1.0
ND2 A:ASN242 4.1 14.3 1.0
O A:HOH577 4.2 14.5 1.0
OE2 A:GLU336 4.3 17.5 1.0
CB A:ASP240 4.4 14.7 1.0
CG A:GLU367 4.4 14.2 1.0
O A:LEU241 4.4 13.0 1.0
O A:HOH542 4.4 20.1 1.0
O A:ILE230 4.5 12.9 1.0
N A:LEU241 4.5 12.2 1.0
OE1 A:GLU336 4.6 16.3 1.0
O A:HOH578 4.6 18.1 1.0
O A:HOH522 4.6 16.5 1.0
C A:LEU241 4.6 13.1 1.0
CD A:GLU336 4.7 16.4 1.0
C A:ASP240 4.8 13.8 1.0
CA A:ASP240 4.8 14.0 1.0
CB A:GLU367 4.8 13.1 1.0
CA A:ASP229 4.8 13.3 1.0
CB A:ASN242 4.9 12.8 1.0
N A:ILE230 4.9 11.8 1.0
CA A:LEU241 4.9 12.8 1.0
C A:ASP229 5.0 12.8 1.0

Cobalt binding site 3 out of 3 in 4ikt

Go back to Cobalt Binding Sites List in 4ikt
Cobalt 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 Cobalt with other atoms in the Co 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:Co404

b:17.8
occ:1.00
 O A:HOH579 2.1 18.3 1.0
N2 A:TFV401 2.2 19.5 1.0
NE2 A:HIS212 2.2 16.4 1.0
O A:HOH578 2.2 18.1 1.0
O A:HOH577 2.2 14.5 1.0
N1 A:TFV401 2.2 19.3 1.0
C6 A:TFV401 3.0 22.8 1.0
C5 A:TFV401 3.0 21.2 1.0
CD2 A:HIS212 3.1 16.4 1.0
C9 A:TFV401 3.1 25.2 1.0
C1 A:TFV401 3.2 15.8 1.0
CE1 A:HIS212 3.2 18.6 1.0
C12 A:TFV401 3.4 22.6 1.0
O A:HOH580 3.9 16.2 1.0
NE2 A:HIS310 4.1 18.1 1.0
O A:HOH517 4.2 13.7 1.0
CG A:HIS212 4.2 15.2 1.0
ND1 A:HIS212 4.3 15.1 1.0
N3 A:TFV401 4.3 26.8 1.0
C4 A:TFV401 4.3 20.1 1.0
C8 A:TFV401 4.4 26.6 1.0
C2 A:TFV401 4.4 15.4 1.0
OD2 A:ASP229 4.5 17.6 1.0
O A:HOH522 4.5 16.5 1.0
CE1 A:HIS310 4.6 20.6 1.0
O A:HOH542 4.7 20.1 1.0
C7 A:TFV401 4.9 28.3 1.0
C3 A:TFV401 4.9 17.5 1.0
OE2 A:GLU336 4.9 17.5 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: Tue Jul 30 17:11:05 2024

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