Atomistry » Zinc » PDB 4k4f-4k98 » 4k4f
Atomistry »
  Zinc »
    PDB 4k4f-4k98 »
      4k4f »

Zinc in PDB 4k4f: Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]

Enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]

All present enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide], PDB code: 4k4f was solved by X.Huang, H.Bregman, C.Wilson, E.Dimauro, H.Gunaydin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.687, 78.121, 146.644, 90.00, 90.00, 90.00
R / Rfree (%) 28 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] (pdb code 4k4f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide], PDB code: 4k4f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4k4f

Go back to Zinc Binding Sites List in 4k4f
Zinc binding site 1 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:24.2
occ:1.00
 ND1 A:HIS1237 2.2 35.7 1.0
SG A:CYS1242 2.4 24.5 1.0
SG A:CYS1234 2.4 34.2 1.0
SG A:CYS1245 2.5 19.1 1.0
CE1 A:HIS1237 2.8 35.6 1.0
CB A:CYS1234 2.9 34.4 1.0
CB A:CYS1242 3.2 22.4 1.0
CG A:HIS1237 3.4 35.8 1.0
CB A:CYS1245 3.6 17.3 1.0
N A:HIS1237 3.9 36.5 1.0
CB A:HIS1237 4.0 35.6 1.0
NE2 A:HIS1237 4.1 35.6 1.0
N A:CYS1245 4.2 17.3 1.0
CD2 A:HIS1237 4.4 35.9 1.0
CA A:CYS1234 4.4 34.7 1.0
CA A:HIS1237 4.5 35.8 1.0
CA A:CYS1245 4.5 17.1 1.0
CA A:CYS1242 4.7 22.2 1.0
CB A:ILE1244 4.7 17.9 1.0
N A:THR1236 4.9 37.3 1.0
C A:THR1236 4.9 36.9 1.0
C A:CYS1234 4.9 35.4 1.0
CB A:THR1236 5.0 37.7 1.0

Zinc binding site 2 out of 2 in 4k4f

Go back to Zinc Binding Sites List in 4k4f
Zinc binding site 2 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:38.0
occ:1.00
 SG B:CYS1242 2.2 31.5 1.0
ND1 B:HIS1237 2.3 37.0 1.0
SG B:CYS1234 2.5 36.3 1.0
SG B:CYS1245 2.5 26.8 1.0
CB B:CYS1234 2.7 36.5 1.0
CB B:CYS1242 3.1 29.8 1.0
CG B:HIS1237 3.2 37.0 1.0
CB B:HIS1237 3.3 37.0 1.0
CE1 B:HIS1237 3.3 37.2 1.0
CB B:CYS1245 3.7 26.0 1.0
N B:HIS1237 3.8 37.1 1.0
CA B:HIS1237 4.1 37.2 1.0
CA B:CYS1234 4.2 36.7 1.0
N B:CYS1245 4.3 25.7 1.0
CD2 B:HIS1237 4.3 37.4 1.0
NE2 B:HIS1237 4.4 37.5 1.0
CA B:CYS1242 4.5 29.7 1.0
CA B:CYS1245 4.7 25.6 1.0
CB B:THR1236 4.8 36.5 1.0
C B:THR1236 4.8 36.8 1.0
C B:HIS1237 4.8 37.1 1.0
C B:CYS1234 4.8 37.3 1.0
N B:CYS1234 4.9 37.2 1.0
CB B:ILE1244 4.9 26.1 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: Sun Oct 27 01:43:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy