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Cobalt in PDB 4iku: Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide

Enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide

All present enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide:
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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide, PDB code: 4iku 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) 34.02 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.493, 77.377, 48.088, 90.00, 90.76, 90.00
R / Rfree (%) 18.9 / 20.4

Other elements in 4iku:

The structure of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide also contains other interesting chemical elements:

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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide (pdb code 4iku). 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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide, PDB code: 4iku:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4iku

Go back to Cobalt Binding Sites List in 4iku
Cobalt binding site 1 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide


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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:10.5
occ:1.00
 O A:HOH578 2.0 8.9 1.0
OE2 A:GLU367 2.0 10.2 1.0
OD2 A:ASP240 2.0 10.4 1.0
NE2 A:HIS303 2.1 11.2 1.0
OE1 A:GLU336 2.2 10.9 1.0
CG A:ASP240 3.0 10.3 1.0
CD A:GLU367 3.0 10.2 1.0
CE1 A:HIS303 3.0 12.1 1.0
CD2 A:HIS303 3.1 13.8 1.0
CD A:GLU336 3.1 10.8 1.0
CO A:CO403 3.1 9.2 1.0
OE1 A:GLU367 3.3 9.4 1.0
OE2 A:GLU336 3.4 12.0 1.0
OD1 A:ASP240 3.4 10.0 1.0
OG1 A:THR334 3.6 12.1 1.0
CG2 A:THR334 3.8 12.1 1.0
O A:HOH501 3.8 9.5 1.0
CB A:THR334 4.0 13.0 1.0
ND1 A:HIS303 4.1 12.6 1.0
CB A:ASP240 4.2 10.7 1.0
CG A:HIS303 4.2 13.4 1.0
O A:HOH528 4.2 10.0 1.0
CG A:GLU367 4.3 10.6 1.0
CG A:GLU336 4.4 11.5 1.0
NE2 A:HIS310 4.8 12.1 1.0
C19 A:SHX401 4.8 15.5 1.0
O A:HOH549 4.8 12.0 1.0
CB A:GLU336 4.9 10.8 1.0
CD2 A:HIS310 4.9 12.7 1.0
OD2 A:ASP229 4.9 9.6 1.0

Cobalt binding site 2 out of 3 in 4iku

Go back to Cobalt Binding Sites List in 4iku
Cobalt binding site 2 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide


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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:9.2
occ:1.00
 OD1 A:ASP240 2.0 10.0 1.0
O A:HOH578 2.0 8.9 1.0
OD1 A:ASP229 2.1 8.7 1.0
OE1 A:GLU367 2.1 9.4 1.0
O A:HOH528 2.3 10.0 1.0
OD2 A:ASP229 2.3 9.6 1.0
CG A:ASP229 2.5 8.8 1.0
CG A:ASP240 2.9 10.3 1.0
CD A:GLU367 3.0 10.2 1.0
OD2 A:ASP240 3.1 10.4 1.0
CO A:CO402 3.1 10.5 1.0
OE2 A:GLU367 3.2 10.2 1.0
O A:HOH501 3.7 9.5 1.0
OG1 A:THR231 4.0 10.8 1.0
CB A:ASP229 4.1 9.0 1.0
ND2 A:ASN242 4.1 8.4 1.0
O A:HOH530 4.1 11.2 1.0
OE2 A:GLU336 4.3 12.0 1.0
CB A:ASP240 4.3 10.7 1.0
O A:HOH527 4.4 13.5 1.0
CG A:GLU367 4.4 10.6 1.0
O A:ILE230 4.5 10.1 1.0
O A:LEU241 4.5 8.5 1.0
OE1 A:GLU336 4.5 10.9 1.0
N A:LEU241 4.5 9.7 1.0
O A:HOH549 4.6 12.0 1.0
O A:HOH519 4.6 10.2 1.0
CD A:GLU336 4.7 10.8 1.0
C A:LEU241 4.7 8.8 1.0
C A:ASP240 4.8 9.8 1.0
CA A:ASP240 4.8 10.4 1.0
CA A:ASP229 4.8 8.8 1.0
CB A:ASN242 4.9 9.3 1.0
N A:ILE230 4.9 9.7 1.0
CB A:GLU367 4.9 9.8 1.0
NE2 A:HIS303 5.0 11.2 1.0
CA A:LEU241 5.0 9.4 1.0
C A:ASP229 5.0 8.9 1.0

Cobalt binding site 3 out of 3 in 4iku

Go back to Cobalt Binding Sites List in 4iku
Cobalt binding site 3 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide


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 2-((5-Chloro-6-Methyl-2- (Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)-3-Phenylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:11.0
occ:1.00
 O A:HOH501 2.1 9.5 1.0
N2 A:SHX401 2.2 12.9 1.0
NE2 A:HIS212 2.2 11.1 1.0
N1 A:SHX401 2.2 12.0 1.0
O A:HOH530 2.2 11.2 1.0
O A:HOH549 2.2 12.0 1.0
C5 A:SHX401 2.9 13.3 1.0
C6 A:SHX401 2.9 13.6 1.0
CD2 A:HIS212 3.1 10.6 1.0
C1 A:SHX401 3.2 11.7 1.0
C7 A:SHX401 3.2 15.2 1.0
CE1 A:HIS212 3.2 12.8 1.0
C19 A:SHX401 3.4 15.5 1.0
O A:HOH578 3.9 8.9 1.0
O A:HOH570 4.0 18.8 1.0
NE2 A:HIS310 4.1 12.1 1.0
O A:HOH528 4.2 10.0 1.0
N3 A:SHX401 4.3 15.1 1.0
CG A:HIS212 4.3 10.3 1.0
C4 A:SHX401 4.3 13.3 1.0
ND1 A:HIS212 4.3 11.7 1.0
C8 A:SHX401 4.4 17.5 1.0
C2 A:SHX401 4.4 12.0 1.0
O A:HOH519 4.4 10.2 1.0
OD2 A:ASP229 4.4 9.6 1.0
CE1 A:HIS310 4.6 12.2 1.0
O A:HOH527 4.7 13.5 1.0
C9 A:SHX401 4.9 17.6 1.0
C3 A:SHX401 4.9 13.1 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: Tue Jul 30 17:11:33 2024

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