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Zinc in PDB 4n4t: Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One]

Enzymatic activity of Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One]

All present enzymatic activity of Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One], PDB code: 4n4t was solved by X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.944, 77.879, 147.647, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One] (pdb code 4n4t). 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 Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One], PDB code: 4n4t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4n4t

Go back to Zinc Binding Sites List in 4n4t
Zinc binding site 1 out of 2 in the Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One]


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 Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:24.8
occ:1.00
 SG A:CYS1234 2.4 25.5 1.0
SG A:CYS1245 2.4 21.6 1.0
ND1 A:HIS1237 2.4 24.5 1.0
SG A:CYS1242 2.4 21.5 1.0
CB A:CYS1234 3.2 25.1 1.0
CE1 A:HIS1237 3.2 24.5 1.0
CB A:CYS1242 3.3 21.6 1.0
CG A:HIS1237 3.4 24.9 1.0
CB A:CYS1245 3.4 20.6 1.0
CB A:HIS1237 3.7 24.8 1.0
N A:HIS1237 3.8 25.6 1.0
N A:CYS1245 4.0 20.6 1.0
O A:HOH1520 4.3 23.5 1.0
CA A:CYS1245 4.3 20.4 1.0
NE2 A:HIS1237 4.3 24.5 1.0
CA A:HIS1237 4.3 25.2 1.0
CD2 A:HIS1237 4.4 24.9 1.0
CB A:THR1236 4.5 26.6 1.0
CB A:ILE1244 4.6 20.6 1.0
CA A:CYS1234 4.7 25.3 1.0
CA A:CYS1242 4.8 21.2 1.0
C A:THR1236 4.8 26.0 1.0
N A:THR1236 5.0 26.1 1.0
CA A:THR1236 5.0 26.3 1.0

Zinc binding site 2 out of 2 in 4n4t

Go back to Zinc Binding Sites List in 4n4t
Zinc binding site 2 out of 2 in the Co-Crystal Structure of Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One]


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 Tankyrase 1 with Compound 3 [(4S)-3-{4-[6- Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Phenyl}-5,5-Dimethyl-4-Phenyl-1, 3-Oxazolidin-2-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:30.4
occ:1.00
 SG B:CYS1245 2.3 24.1 1.0
ND1 B:HIS1237 2.4 32.4 1.0
SG B:CYS1234 2.4 31.5 1.0
SG B:CYS1242 2.4 25.9 1.0
CB B:CYS1234 3.0 31.3 1.0
CG B:HIS1237 3.2 32.6 1.0
CB B:CYS1245 3.3 24.6 1.0
CE1 B:HIS1237 3.3 32.5 1.0
CB B:CYS1242 3.3 26.6 1.0
CB B:HIS1237 3.4 32.5 1.0
N B:HIS1237 3.8 32.8 1.0
N B:CYS1245 3.9 24.6 1.0
CA B:HIS1237 4.2 32.6 1.0
O B:HOH1514 4.2 25.3 1.0
CA B:CYS1245 4.3 24.8 1.0
CD2 B:HIS1237 4.3 32.4 1.0
NE2 B:HIS1237 4.3 32.5 1.0
CA B:CYS1234 4.5 31.4 1.0
CB B:THR1236 4.6 32.4 1.0
CB B:ILE1244 4.7 24.8 1.0
CA B:CYS1242 4.8 26.8 1.0
C B:THR1236 4.8 32.7 1.0
C B:HIS1237 4.9 32.6 1.0
C B:CYS1234 5.0 31.5 1.0

Reference:

H.Huang, A.Guzman-Perez, L.Acquaviva, V.Berry, H.Bregman, J.Dovey, H.Gunaydin, X.Huang, L.Huang, D.Saffran, R.Serafino, S.Schneider, C.Wilson, E.F.Dimauro. Structure-Based Design of 2-Aminopyridine Oxazolidinones As Potent and Selective Tankyrase Inhibitors. Acs Med Chem Lett V. 4 1218 2013.
ISSN: ISSN 1948-5875
PubMed: 24900633
DOI: 10.1021/ML4003315
Page generated: Sun Oct 27 03:00:54 2024

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