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Zinc in PDB 4li8: Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide

Enzymatic activity of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide

All present enzymatic activity of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide:
2.4.2.30;

Protein crystallography data

The structure of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide, PDB code: 4li8 was solved by C.A.Kirby, T.Stams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.04 / 2.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.700, 43.100, 88.100, 90.00, 91.30, 90.00
R / Rfree (%) 20.7 / 28.3

Other elements in 4li8:

The structure of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide (pdb code 4li8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide, PDB code: 4li8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4li8

Go back to Zinc Binding Sites List in 4li8
Zinc binding site 1 out of 2 in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:45.2
occ:1.00
 SG A:CYS1234 2.3 32.4 1.0
ND1 A:HIS1237 2.4 42.0 1.0
SG A:CYS1242 2.4 32.2 1.0
SG A:CYS1245 2.5 47.2 1.0
CB A:CYS1234 3.0 40.2 1.0
CG A:HIS1237 3.2 39.8 1.0
CB A:CYS1242 3.2 35.5 1.0
CE1 A:HIS1237 3.4 41.3 1.0
CB A:HIS1237 3.4 34.8 1.0
CB A:CYS1245 3.4 39.2 1.0
N A:HIS1237 3.7 39.6 1.0
N A:CYS1245 4.1 36.8 1.0
CA A:HIS1237 4.1 37.0 1.0
CB A:THR1236 4.3 38.9 1.0
CA A:CYS1245 4.4 44.8 1.0
CD2 A:HIS1237 4.4 45.7 1.0
NE2 A:HIS1237 4.5 43.1 1.0
CA A:CYS1234 4.5 36.9 1.0
CA A:CYS1242 4.7 32.1 1.0
CB A:ILE1244 4.7 34.4 1.0
C A:THR1236 4.7 45.1 1.0
C A:HIS1237 4.9 39.0 1.0
CA A:THR1236 4.9 45.0 1.0
CB A:ASP1239 4.9 30.2 1.0
C A:CYS1234 4.9 37.3 1.0
CG2 A:THR1236 4.9 36.6 1.0
N A:THR1236 4.9 38.7 1.0

Zinc binding site 2 out of 2 in 4li8

Go back to Zinc Binding Sites List in 4li8
Zinc binding site 2 out of 2 in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:40.4
occ:1.00
 SG B:CYS1242 2.2 37.6 1.0
SG B:CYS1245 2.3 36.6 1.0
ND1 B:HIS1237 2.4 45.6 1.0
SG B:CYS1234 2.5 43.9 1.0
CG B:HIS1237 2.9 43.9 1.0
CE1 B:HIS1237 3.2 41.2 1.0
CB B:HIS1237 3.2 43.2 1.0
CB B:CYS1245 3.3 39.5 1.0
CB B:CYS1242 3.4 37.2 1.0
CB B:CYS1234 3.8 38.3 1.0
N B:CYS1245 3.9 36.3 1.0
CD2 B:HIS1237 3.9 46.5 1.0
O B:HOH1524 3.9 43.4 1.0
N B:HIS1237 3.9 41.5 1.0
NE2 B:HIS1237 4.0 40.6 1.0
CA B:CYS1245 4.1 34.3 1.0
CA B:HIS1237 4.2 42.6 1.0
CB B:ILE1244 4.3 40.9 1.0
CB B:THR1236 4.5 52.2 1.0
CA B:CYS1242 4.7 36.9 1.0
C B:ILE1244 4.8 40.5 1.0
C B:THR1236 4.9 43.3 1.0
CG2 B:ILE1244 4.9 38.1 1.0
CD1 B:ILE1244 5.0 36.9 1.0
CB B:ASP1239 5.0 39.5 1.0
N B:ILE1244 5.0 34.9 1.0

Reference:

M.D.Shultz, A.K.Cheung, C.A.Kirby, B.Firestone, J.Fan, C.H.Chen, Z.Chen, D.N.Chin, L.Dipietro, A.Fazal, Y.Feng, P.D.Fortin, T.Gould, B.Lagu, H.Lei, F.Lenoir, D.Majumdar, E.Ochala, M.G.Palermo, L.Pham, M.Pu, T.Smith, T.Stams, R.C.Tomlinson, B.B.Toure, M.Visser, R.M.Wang, N.J.Waters, W.Shao. Identification of Nvp-TNKS656: the Use of Structure-Efficiency Relationships to Generate A Highly Potent, Selective, and Orally Active Tankyrase Inhibitor. J.Med.Chem. V. 56 6495 2013.
ISSN: ISSN 0022-2623
PubMed: 23844574
DOI: 10.1021/JM400807N
Page generated: Sun Oct 27 01:51:26 2024

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