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Zinc in PDB 5al3: Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One

Enzymatic activity of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One

All present enzymatic activity of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One:
2.4.2.30;

Protein crystallography data

The structure of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One, PDB code: 5al3 was solved by Y.Nkizinkiko, L.Lehtio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.620, 98.570, 118.760, 90.00, 90.00, 90.00
R / Rfree (%) 15.873 / 19.309

Other elements in 5al3:

The structure of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One (pdb code 5al3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One, PDB code: 5al3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5al3

Go back to Zinc Binding Sites List in 5al3
Zinc binding site 1 out of 2 in the Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3162

b:24.0
occ:1.00
 ND1 A:HIS1084 2.2 26.3 1.0
SG A:CYS1081 2.2 22.7 1.0
SG A:CYS1089 2.3 22.6 1.0
SG A:CYS1092 2.3 24.9 1.0
CE1 A:HIS1084 3.0 27.3 1.0
CG A:HIS1084 3.2 27.4 1.0
CB A:CYS1092 3.2 24.5 1.0
CB A:CYS1081 3.3 23.6 1.0
CB A:CYS1089 3.3 21.0 1.0
CB A:HIS1084 3.6 26.1 1.0
N A:HIS1084 3.9 27.9 1.0
N A:CYS1092 4.0 21.3 1.0
O A:HOH2139 4.1 33.1 1.0
NE2 A:HIS1084 4.2 27.0 1.0
CA A:CYS1092 4.2 23.5 1.0
CD2 A:HIS1084 4.3 26.2 1.0
CB A:VAL1083 4.3 30.2 1.0
CA A:HIS1084 4.3 26.3 1.0
CA A:CYS1089 4.7 20.6 1.0
CA A:CYS1081 4.7 24.2 1.0
C A:VAL1083 4.8 30.8 1.0
CG1 A:VAL1083 4.8 31.8 1.0
O A:HOH2131 4.9 28.6 1.0
CA A:VAL1083 4.9 28.7 1.0
CB A:ILE1091 4.9 27.0 1.0
N A:VAL1083 4.9 27.7 1.0

Zinc binding site 2 out of 2 in 5al3

Go back to Zinc Binding Sites List in 5al3
Zinc binding site 2 out of 2 in the Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TNKS2 in Complex with 2-(2,4- Dichlorophenyl)-1-Methyl-1H,2H,3H,4H-Pyrido(2,3-D) Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3162

b:21.5
occ:1.00
 ND1 B:HIS1084 2.1 23.4 1.0
SG B:CYS1089 2.3 20.7 1.0
SG B:CYS1081 2.3 20.3 1.0
SG B:CYS1092 2.4 22.7 1.0
CE1 B:HIS1084 3.1 24.0 1.0
CG B:HIS1084 3.2 23.7 1.0
CB B:CYS1092 3.3 22.1 1.0
CB B:CYS1081 3.3 20.1 1.0
CB B:CYS1089 3.3 19.8 1.0
CB B:HIS1084 3.5 22.2 1.0
N B:HIS1084 3.9 23.0 1.0
N B:CYS1092 4.0 19.6 1.0
O B:HOH2126 4.2 25.8 1.0
NE2 B:HIS1084 4.2 25.7 1.0
O B:HOH2119 4.2 40.3 1.0
CA B:CYS1092 4.2 21.5 1.0
CD2 B:HIS1084 4.3 24.6 1.0
CA B:HIS1084 4.3 22.1 1.0
CB B:VAL1083 4.4 27.0 1.0
CA B:CYS1089 4.7 18.3 1.0
CA B:CYS1081 4.7 20.6 1.0
CB B:ILE1091 4.7 23.5 1.0
C B:VAL1083 4.8 25.5 1.0
N B:VAL1083 4.9 24.4 1.0
O B:HOH2113 4.9 21.1 1.0
CA B:VAL1083 4.9 26.1 1.0
CG1 B:VAL1083 4.9 28.2 1.0

Reference:

Y.Nkizinkiko, B.V.S.Suneel Kumar, V.U.Jeankumar, T.Haikarainen, J.Koivunen, C.Madhuri, P.Yogeeswari, H.Venkannagari, E.Obaji, T.Pihlajaniemi, D.Sriram, L.Lehtio. Discovery of Potent and Selective Nonplanar Tankyrase Inhibiting Nicotinamide Mimics. Bioorg.Med.Chem. V. 23 4139 2015.
ISSN: ISSN 0968-0896
PubMed: 26183543
DOI: 10.1016/J.BMC.2015.06.063
Page generated: Sun Oct 27 13:03:58 2024

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