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

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-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine (pdb code 4iks). 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-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine, PDB code: 4iks:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4iks

Go back to Cobalt Binding Sites List in 4iks
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-(6-(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-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:12.6
occ:1.00
 O A:HOH586 1.9 12.4 1.0
OE2 A:GLU367 2.0 9.6 1.0
NE2 A:HIS303 2.1 7.7 1.0
OD2 A:ASP240 2.1 8.6 1.0
OE1 A:GLU336 2.2 13.4 1.0
CD A:GLU367 2.9 10.4 1.0
CE1 A:HIS303 3.0 12.8 1.0
CG A:ASP240 3.0 10.5 1.0
CD2 A:HIS303 3.1 12.7 1.0
CO A:CO403 3.1 11.3 1.0
CD A:GLU336 3.1 12.3 1.0
OE1 A:GLU367 3.2 12.1 1.0
OD1 A:ASP240 3.3 8.5 1.0
OE2 A:GLU336 3.5 12.1 1.0
OG1 A:THR334 3.7 13.1 1.0
O A:HOH588 3.8 16.8 1.0
CG2 A:THR334 3.8 12.6 1.0
CB A:THR334 4.1 13.4 1.0
ND1 A:HIS303 4.1 12.7 1.0
CG A:HIS303 4.2 13.7 1.0
CB A:ASP240 4.2 10.9 1.0
CG A:GLU367 4.3 9.4 1.0
O A:HOH534 4.3 14.0 1.0
CG A:GLU336 4.4 11.3 1.0
NE2 A:HIS310 4.7 15.8 1.0
OD2 A:ASP229 4.8 12.3 1.0
O A:HOH587 4.9 20.9 1.0
CB A:GLU336 4.9 10.2 1.0
CD2 A:HIS310 4.9 17.0 1.0

Cobalt binding site 2 out of 3 in 4iks

Go back to Cobalt Binding Sites List in 4iks
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-(6-(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-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:11.3
occ:1.00
 OE1 A:GLU367 2.0 12.1 1.0
OD1 A:ASP240 2.1 8.5 1.0
O A:HOH586 2.1 12.4 1.0
OD1 A:ASP229 2.1 9.7 1.0
OD2 A:ASP229 2.3 12.3 1.0
O A:HOH534 2.4 14.0 1.0
CG A:ASP229 2.5 11.4 1.0
CG A:ASP240 3.0 10.5 1.0
CD A:GLU367 3.0 10.4 1.0
CO A:CO402 3.1 12.6 1.0
OD2 A:ASP240 3.2 8.6 1.0
OE2 A:GLU367 3.3 9.6 1.0
O A:HOH588 3.8 16.8 1.0
CB A:ASP229 4.0 10.7 1.0
OG1 A:THR231 4.0 11.5 1.0
ND2 A:ASN242 4.1 11.1 1.0
O A:HOH585 4.1 14.6 1.0
OE2 A:GLU336 4.3 12.1 1.0
O A:LEU241 4.4 11.0 1.0
CB A:ASP240 4.4 10.9 1.0
O A:HOH557 4.4 18.9 1.0
CG A:GLU367 4.4 9.4 1.0
OE1 A:GLU336 4.5 13.4 1.0
O A:ILE230 4.5 9.8 1.0
O A:HOH512 4.6 13.9 1.0
N A:LEU241 4.6 9.5 1.0
C A:LEU241 4.7 11.0 1.0
O A:HOH587 4.7 20.9 1.0
CD A:GLU336 4.7 12.3 1.0
C A:ASP240 4.8 11.1 1.0
CA A:ASP229 4.8 10.8 1.0
CA A:ASP240 4.8 11.1 1.0
CB A:ASN242 4.9 10.1 1.0
CB A:GLU367 4.9 9.4 1.0
N A:ILE230 4.9 9.8 1.0
CA A:LEU241 5.0 10.9 1.0
NE2 A:HIS303 5.0 7.7 1.0
C A:ASP229 5.0 10.3 1.0
CG A:ASN242 5.0 11.2 1.0

Cobalt binding site 3 out of 3 in 4iks

Go back to Cobalt Binding Sites List in 4iks
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-(6-(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-(6-(Trifluoromethyl)Pyridin-2-Yl) Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:16.2
occ:1.00
 N2 A:TFD401 2.1 20.4 0.5
NE2 A:HIS212 2.1 12.2 1.0
O A:HOH588 2.2 16.8 1.0
N1 A:TFD401 2.2 11.9 0.5
O A:HOH587 2.2 20.9 1.0
N2 A:TFD401 2.2 9.4 0.5
O A:HOH585 2.3 14.6 1.0
N1 A:TFD401 2.3 20.1 0.5
C6 A:TFD401 2.9 21.2 0.5
C5 A:TFD401 2.9 12.7 0.5
C5 A:TFD401 2.9 20.5 0.5
C6 A:TFD401 3.0 12.4 0.5
CD2 A:HIS212 3.1 11.7 1.0
C9 A:TFD401 3.1 23.1 0.5
CE1 A:HIS212 3.1 14.2 1.0
C1 A:TFD401 3.2 11.4 0.5
C1 A:TFD401 3.3 19.6 0.5
C9 A:TFD401 3.3 15.6 0.5
C12 A:TFD401 3.4 23.3 0.5
C12 A:TFD401 3.6 15.8 0.5
O A:HOH631 3.8 30.1 1.0
O A:HOH586 3.9 12.4 1.0
NE2 A:HIS310 4.0 15.8 1.0
N3 A:TFD401 4.2 22.8 0.5
CG A:HIS212 4.2 12.0 1.0
ND1 A:HIS212 4.2 13.2 1.0
C4 A:TFD401 4.2 12.3 0.5
O A:HOH534 4.3 14.0 1.0
C4 A:TFD401 4.3 19.9 0.5
N3 A:TFD401 4.3 13.3 0.5
C8 A:TFD401 4.3 23.4 0.5
C2 A:TFD401 4.4 11.6 0.5
CE1 A:HIS310 4.5 16.6 1.0
C2 A:TFD401 4.5 19.2 0.5
C8 A:TFD401 4.5 16.2 0.5
O A:HOH512 4.6 13.9 1.0
OD2 A:ASP229 4.6 12.3 1.0
C7 A:TFD401 4.8 23.6 0.5
C3 A:TFD401 4.9 12.0 0.5
O A:HOH557 4.9 18.9 1.0
C3 A:TFD401 4.9 19.3 0.5
C7 A:TFD401 4.9 15.8 0.5
OE2 A:GLU336 5.0 12.1 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 10:44:36 2020

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