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Chlorine in PDB 4k4e: Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]

Enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]

All present enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide], PDB code: 4k4e was solved by X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.12 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.440, 73.264, 149.059, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28

Other elements in 4k4e:

The structure of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] (pdb code 4k4e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide], PDB code: 4k4e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4k4e

Go back to Chlorine Binding Sites List in 4k4e
Chlorine binding site 1 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1402

b:37.8
occ:1.00
 CL1 A:K4E1402 0.0 37.8 1.0
C3 A:K4E1402 1.8 36.9 1.0
C4 A:K4E1402 2.6 37.3 1.0
C2 A:K4E1402 2.8 35.8 1.0
O A:TYR1224 3.4 26.7 1.0
C A:GLY1227 3.4 29.6 1.0
CD2 A:TYR1224 3.6 39.5 1.0
N A:ILE1228 3.6 29.6 1.0
CA A:GLY1227 3.6 28.0 1.0
CB A:TYR1224 3.8 32.1 1.0
O A:GLY1227 3.8 29.8 1.0
CD A:PRO1187 3.9 31.2 1.0
C5 A:K4E1402 4.0 39.0 1.0
C1 A:K4E1402 4.1 36.9 1.0
N A:GLY1227 4.1 28.2 1.0
CA A:SER1186 4.1 26.9 1.0
CG A:TYR1224 4.2 36.8 1.0
CA A:ILE1228 4.2 29.9 1.0
C A:TYR1224 4.2 28.1 1.0
CG1 A:ILE1228 4.3 32.0 1.0
CA A:TYR1224 4.3 27.9 1.0
CB A:SER1186 4.3 26.9 1.0
CG A:PRO1187 4.5 29.6 1.0
C6 A:K4E1402 4.6 37.9 1.0
O A:HOH1529 4.6 30.8 1.0
CE2 A:TYR1224 4.6 41.0 1.0
O A:GLY1185 4.6 25.0 1.0
N A:PRO1187 4.9 28.4 1.0
CB A:ILE1228 5.0 31.4 1.0

Chlorine binding site 2 out of 2 in 4k4e

Go back to Chlorine Binding Sites List in 4k4e
Chlorine binding site 2 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1402

b:49.2
occ:1.00
 CL1 B:K4E1402 0.0 49.2 1.0
C3 B:K4E1402 1.7 44.7 1.0
C4 B:K4E1402 2.6 44.5 1.0
C2 B:K4E1402 2.7 42.8 1.0
CB B:TYR1224 3.3 42.8 1.0
O B:TYR1224 3.5 39.0 1.0
CD1 B:TYR1224 3.7 46.0 1.0
N B:ILE1228 3.7 46.6 1.0
C B:GLY1227 3.8 45.4 1.0
CA B:GLY1227 3.9 43.9 1.0
CG B:TYR1224 3.9 44.6 1.0
CD B:PRO1187 3.9 31.7 1.0
C5 B:K4E1402 4.0 45.1 1.0
CB B:SER1186 4.0 31.0 1.0
C1 B:K4E1402 4.0 42.6 1.0
CA B:TYR1224 4.1 40.9 1.0
CA B:SER1186 4.1 29.8 1.0
C B:TYR1224 4.2 39.8 1.0
N B:GLY1227 4.3 42.1 1.0
O B:GLY1185 4.4 30.0 1.0
CG1 B:ILE1228 4.4 49.0 1.0
CA B:ILE1228 4.4 47.8 1.0
O B:GLY1227 4.5 45.1 1.0
C6 B:K4E1402 4.5 43.1 1.0
CE1 B:TYR1224 4.9 48.2 1.0
CG B:PRO1187 5.0 32.2 1.0
N B:PRO1187 5.0 30.5 1.0

Reference:

H.Bregman, N.Chakka, A.Guzman-Perez, H.Gunaydin, Y.Gu, X.Huang, V.Berry, J.Liu, Y.Teffera, L.Huang, B.Egge, E.L.Mullady, S.Schneider, P.S.Andrews, A.Mishra, J.Newcomb, R.Serafino, C.A.Strathdee, S.M.Turci, C.Wilson, E.F.Dimauro. Discovery of Novel, Induced-Pocket Binding Oxazolidinones As Potent, Selective, and Orally Bioavailable Tankyrase Inhibitors. J.Med.Chem. V. 56 4320 2013.
ISSN: ISSN 0022-2623
PubMed: 23701517
DOI: 10.1021/JM4000038
Page generated: Fri Jul 11 17:39:29 2025

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