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Chlorine 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:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5al3

Go back to Chlorine Binding Sites List in 5al3
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl3168

b:23.2
occ:1.00
 CL1 A:TGW3168 0.0 23.2 1.0
CAB A:TGW3168 1.8 24.7 1.0
CAC A:TGW3168 2.8 25.6 1.0
CAH A:TGW3168 2.8 23.4 1.0
CAI A:TGW3168 3.2 21.2 1.0
N A:TYR1060 3.3 15.9 1.0
O A:HIS1048 3.5 26.4 1.0
N A:TYR1050 3.6 23.0 1.0
O A:GLY1058 3.6 19.8 1.0
CE1 A:HIS1031 3.7 17.2 1.0
CB A:TYR1050 3.7 24.0 1.0
CA A:ILE1059 3.8 17.8 1.0
CAT A:TGW3168 3.8 21.1 1.0
CD1 A:TYR1060 4.0 18.0 1.0
C A:ILE1059 4.1 16.0 1.0
CB A:TYR1060 4.1 16.4 1.0
CAD A:TGW3168 4.1 25.7 1.0
NAS A:TGW3168 4.1 20.3 1.0
CAG A:TGW3168 4.1 23.6 1.0
C A:ALA1049 4.1 26.4 1.0
CA A:TYR1060 4.2 16.1 1.0
CA A:ALA1049 4.3 24.5 1.0
CA A:TYR1050 4.3 23.6 1.0
CG2 A:ILE1059 4.4 20.1 1.0
O A:TYR1060 4.4 16.4 1.0
NAJ A:TGW3168 4.4 18.7 1.0
O A:HOH2095 4.5 22.6 1.0
CG A:TYR1060 4.5 17.2 1.0
NE2 A:HIS1031 4.5 17.5 1.0
C A:HIS1048 4.6 25.9 1.0
C A:GLY1058 4.6 18.7 1.0
CAF A:TGW3168 4.6 25.3 1.0
CB A:ILE1059 4.6 19.9 1.0
ND1 A:HIS1031 4.7 16.3 1.0
N A:ILE1059 4.7 17.0 1.0
C A:TYR1060 4.8 16.0 1.0
O A:ALA1049 4.9 28.2 1.0
N A:ALA1049 4.9 24.3 1.0
CAR A:TGW3168 4.9 18.8 1.0
CG A:TYR1050 5.0 22.6 1.0

Chlorine binding site 2 out of 4 in 5al3

Go back to Chlorine Binding Sites List in 5al3
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl3168

b:33.0
occ:1.00
 CL2 A:TGW3168 0.0 33.0 1.0
CAD A:TGW3168 1.8 25.7 1.0
CAF A:TGW3168 2.7 25.3 1.0
CAC A:TGW3168 2.8 25.6 1.0
CE2 A:PHE1035 3.5 37.6 1.0
CD2 A:PHE1035 3.8 36.3 1.0
CD A:PRO1034 3.9 21.1 1.0
CAG A:TGW3168 4.0 23.6 1.0
OG A:SER1033 4.1 21.5 1.0
CAB A:TGW3168 4.1 24.7 1.0
CD1 A:ILE1075 4.2 30.1 1.0
CG A:PRO1034 4.5 23.4 1.0
CAH A:TGW3168 4.6 23.4 1.0
O A:HOH2095 4.6 22.6 1.0
CZ A:PHE1035 4.6 39.4 1.0
O A:HIS1048 4.8 26.4 1.0
CG1 A:ILE1075 4.8 27.9 1.0
O A:ALA1049 4.9 28.2 1.0
O A:HOH2133 4.9 37.0 1.0

Chlorine binding site 3 out of 4 in 5al3

Go back to Chlorine Binding Sites List in 5al3
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl3166

b:26.2
occ:1.00
 CL1 B:TGW3166 0.0 26.2 1.0
CAB B:TGW3166 1.8 30.6 1.0
CAC B:TGW3166 2.7 30.5 1.0
CAH B:TGW3166 2.9 27.2 1.0
CAI B:TGW3166 3.2 25.6 1.0
N B:TYR1060 3.3 18.0 1.0
O B:HIS1048 3.4 32.3 1.0
N B:TYR1050 3.6 28.6 1.0
CE1 B:HIS1031 3.7 19.1 1.0
CB B:TYR1050 3.7 28.5 1.0
CA B:ILE1059 3.8 20.9 1.0
O B:GLY1058 3.8 22.5 1.0
CAT B:TGW3166 3.9 25.5 1.0
C B:ILE1059 4.0 18.8 1.0
CB B:TYR1060 4.0 18.1 1.0
CAD B:TGW3166 4.1 30.3 1.0
CD1 B:TYR1060 4.1 20.3 1.0
CAG B:TGW3166 4.1 27.7 1.0
C B:ALA1049 4.1 31.0 1.0
NAS B:TGW3166 4.2 25.9 1.0
CA B:TYR1060 4.2 17.9 1.0
CA B:TYR1050 4.3 29.2 1.0
CA B:ALA1049 4.3 31.9 1.0
CG2 B:ILE1059 4.3 22.7 1.0
O B:TYR1060 4.3 18.8 1.0
NAJ B:TGW3166 4.4 24.7 1.0
O B:HOH2086 4.4 26.4 1.0
NE2 B:HIS1031 4.5 18.0 1.0
C B:HIS1048 4.5 32.0 1.0
CG B:TYR1060 4.5 19.8 1.0
CB B:ILE1059 4.6 22.7 1.0
CAF B:TGW3166 4.6 29.2 1.0
ND1 B:HIS1031 4.6 17.5 1.0
C B:GLY1058 4.7 20.7 1.0
N B:ILE1059 4.7 22.4 1.0
C B:TYR1060 4.8 16.6 1.0
N B:ALA1049 4.9 31.1 1.0
O B:ALA1049 4.9 31.5 1.0
CG B:TYR1050 5.0 28.2 1.0
CAR B:TGW3166 5.0 25.5 1.0

Chlorine binding site 4 out of 4 in 5al3

Go back to Chlorine Binding Sites List in 5al3
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl3166

b:38.4
occ:1.00
 CL2 B:TGW3166 0.0 38.4 1.0
CAD B:TGW3166 1.7 30.3 1.0
CAF B:TGW3166 2.7 29.2 1.0
CAC B:TGW3166 2.8 30.5 1.0
CE2 B:PHE1035 3.4 45.5 1.0
CD2 B:PHE1035 3.8 41.0 1.0
CD B:PRO1034 3.9 25.6 1.0
CAG B:TGW3166 4.0 27.7 1.0
OG B:SER1033 4.0 24.1 1.0
CAB B:TGW3166 4.1 30.6 1.0
CD1 B:ILE1075 4.3 28.4 1.0
CZ B:PHE1035 4.3 46.4 1.0
O B:HOH2086 4.4 26.4 1.0
CAH B:TGW3166 4.5 27.2 1.0
CG B:PRO1034 4.6 28.3 1.0
O B:HIS1048 4.8 32.3 1.0
CG1 B:ILE1075 4.8 27.9 1.0
O B:ALA1049 4.9 31.5 1.0
CB B:SER1033 4.9 21.9 1.0
O B:HOH2116 4.9 33.8 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: Sat Jul 12 00:15:02 2025

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