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Fluorine in PDB 3mhj: Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One

Enzymatic activity of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One

All present enzymatic activity of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One:
2.4.2.30;

Protein crystallography data

The structure of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One, PDB code: 3mhj was solved by T.Karlberg, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Kotenyova, N.Markova, M.Moche, P.Nordlund, T.Nyman, C.Persson, M.I.Siponen, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, H.Schuler, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.21 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.547, 97.727, 119.126, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.3

Other elements in 3mhj:

The structure of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One (pdb code 3mhj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One, PDB code: 3mhj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3mhj

Go back to Fluorine Binding Sites List in 3mhj
Fluorine binding site 1 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:31.4
occ:1.00
 FAC A:M3F2 0.0 31.4 1.0
CAT A:M3F2 1.3 27.1 1.0
FAD A:M3F2 2.1 27.5 1.0
FAE A:M3F2 2.2 31.0 1.0
CAN A:M3F2 2.3 26.6 1.0
NAK A:M3F2 2.8 21.2 1.0
CAJ A:M3F2 3.4 21.8 1.0
CE2 A:PHE1035 3.4 38.8 1.0
CB A:SER1033 3.6 20.5 1.0
CD2 A:PHE1035 3.7 34.4 1.0
O A:HOH53 3.8 21.1 1.0
CAQ A:M3F2 4.0 19.7 1.0
O A:HOH315 4.0 28.3 1.0
OG A:SER1033 4.2 23.2 1.0
CAM A:M3F2 4.6 22.7 1.0
CE1 A:HIS1031 4.6 18.4 1.0
CZ A:PHE1035 4.7 40.6 1.0
CD1 A:ILE1051 4.7 49.7 1.0
CD A:PRO1034 4.7 21.9 1.0
CA A:SER1033 4.8 19.8 1.0
NAL A:M3F2 4.8 17.4 1.0
CAS A:M3F2 4.9 19.4 1.0
NE2 A:HIS1031 4.9 17.9 1.0
O A:GLY1032 4.9 19.9 1.0

Fluorine binding site 2 out of 6 in 3mhj

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Fluorine binding site 2 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:27.5
occ:1.00
 FAD A:M3F2 0.0 27.5 1.0
CAT A:M3F2 1.3 27.1 1.0
FAC A:M3F2 2.1 31.4 1.0
FAE A:M3F2 2.2 31.0 1.0
CAN A:M3F2 2.3 26.6 1.0
NAK A:M3F2 2.8 21.2 1.0
CAJ A:M3F2 3.4 21.8 1.0
CB A:SER1033 3.7 20.5 1.0
CD A:PRO1034 3.8 21.9 1.0
CD1 A:TYR1071 4.0 17.6 1.0
CAQ A:M3F2 4.1 19.7 1.0
CG1 A:ILE1075 4.2 28.0 1.0
O A:TYR1071 4.2 15.5 1.0
CB A:TYR1071 4.2 14.7 1.0
N A:ILE1075 4.3 22.1 1.0
CA A:SER1033 4.4 19.8 1.0
CE2 A:PHE1035 4.5 38.8 1.0
C A:GLY1074 4.5 20.7 1.0
CAM A:M3F2 4.5 22.7 1.0
CG A:TYR1071 4.5 15.8 1.0
O A:GLY1032 4.6 19.9 1.0
CA A:GLY1074 4.6 19.9 1.0
CD1 A:ILE1075 4.7 32.7 1.0
CG A:PRO1034 4.8 24.8 1.0
CAS A:M3F2 4.8 19.4 1.0
NAL A:M3F2 4.9 17.4 1.0
OG A:SER1033 4.9 23.2 1.0
CD2 A:PHE1035 4.9 34.4 1.0
N A:PRO1034 4.9 21.8 1.0
CE1 A:TYR1071 5.0 18.9 1.0
CA A:ILE1075 5.0 22.6 1.0

Fluorine binding site 3 out of 6 in 3mhj

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Fluorine binding site 3 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:31.0
occ:1.00
 FAE A:M3F2 0.0 31.0 1.0
CAT A:M3F2 1.3 27.1 1.0
FAD A:M3F2 2.2 27.5 1.0
FAC A:M3F2 2.2 31.4 1.0
CAN A:M3F2 2.4 26.6 1.0
CAJ A:M3F2 2.7 21.8 1.0
CG2 A:ILE1051 3.4 50.1 1.0
NAK A:M3F2 3.6 21.2 1.0
CD1 A:ILE1075 3.6 32.7 1.0
CG1 A:ILE1075 3.6 28.0 1.0
CD1 A:ILE1051 3.7 49.7 1.0
CAM A:M3F2 4.1 22.7 1.0
CB A:ILE1051 4.2 49.5 1.0
CE2 A:PHE1035 4.5 38.8 1.0
CG1 A:ILE1051 4.5 50.3 1.0
CAQ A:M3F2 4.7 19.7 1.0
O A:HOH53 4.8 21.1 1.0
CD1 A:TYR1071 4.9 17.6 1.0
O A:HOH185 5.0 40.4 1.0
CAS A:M3F2 5.0 19.4 1.0
CAA A:M3F2 5.0 24.4 1.0

Fluorine binding site 4 out of 6 in 3mhj

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Fluorine binding site 4 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:28.1
occ:1.00
 FAC B:M3F2 0.0 28.1 1.0
CAT B:M3F2 1.3 25.2 1.0
FAD B:M3F2 2.1 24.4 1.0
FAE B:M3F2 2.2 28.1 1.0
CAN B:M3F2 2.4 21.2 1.0
NAK B:M3F2 2.8 17.4 1.0
CAJ B:M3F2 3.5 21.3 1.0
CB B:SER1033 3.5 19.4 1.0
CE2 B:PHE1035 3.6 33.0 1.0
O B:ALA1049 3.7 28.7 0.5
CD2 B:PHE1035 3.8 28.4 1.0
O B:HOH13 3.9 16.7 1.0
O B:HIS1048 4.0 24.2 0.5
CAQ B:M3F2 4.1 17.3 1.0
OG B:SER1033 4.2 19.2 1.0
CE1 B:HIS1031 4.6 16.9 1.0
CAM B:M3F2 4.7 21.8 1.0
C B:HIS1048 4.7 26.6 0.5
C B:ALA1049 4.7 28.4 0.5
CA B:SER1033 4.7 17.1 1.0
CB B:TYR1050 4.8 31.1 0.5
CD B:PRO1034 4.8 20.0 1.0
NE2 B:HIS1031 4.8 15.4 1.0
CZ B:PHE1035 4.8 33.7 1.0
NAL B:M3F2 4.9 15.2 1.0
CD1 B:ILE1075 4.9 29.8 1.0
O B:GLY1032 4.9 17.7 1.0
CAS B:M3F2 4.9 15.5 1.0

Fluorine binding site 5 out of 6 in 3mhj

Go back to Fluorine Binding Sites List in 3mhj
Fluorine binding site 5 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:24.4
occ:1.00
 FAD B:M3F2 0.0 24.4 1.0
CAT B:M3F2 1.3 25.2 1.0
FAC B:M3F2 2.1 28.1 1.0
FAE B:M3F2 2.2 28.1 1.0
CAN B:M3F2 2.3 21.2 1.0
NAK B:M3F2 2.8 17.4 1.0
CAJ B:M3F2 3.4 21.3 1.0
CD1 B:ILE1075 3.6 29.8 1.0
CB B:SER1033 3.7 19.4 1.0
CD B:PRO1034 3.8 20.0 1.0
CAQ B:M3F2 4.1 17.3 1.0
CD1 B:TYR1071 4.1 18.0 1.0
CA B:SER1033 4.3 17.1 1.0
O B:TYR1071 4.3 16.0 1.0
CB B:TYR1071 4.4 14.4 1.0
CG1 B:ILE1075 4.5 23.8 1.0
N B:ILE1075 4.5 19.2 1.0
CAM B:M3F2 4.6 21.8 1.0
O B:GLY1032 4.6 17.7 1.0
C B:GLY1074 4.6 18.7 1.0
CE2 B:PHE1035 4.6 33.0 1.0
CG B:TYR1071 4.7 14.4 1.0
CA B:GLY1074 4.7 18.9 1.0
OG B:SER1033 4.8 19.2 1.0
O B:HOH98 4.8 35.6 1.0
N B:PRO1034 4.9 19.3 1.0
CAS B:M3F2 4.9 15.5 1.0
NAL B:M3F2 4.9 15.2 1.0
CG B:PRO1034 4.9 21.4 1.0
CD2 B:PHE1035 4.9 28.4 1.0

Fluorine binding site 6 out of 6 in 3mhj

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Fluorine binding site 6 out of 6 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:28.1
occ:1.00
 FAE B:M3F2 0.0 28.1 1.0
CAT B:M3F2 1.3 25.2 1.0
FAD B:M3F2 2.2 24.4 1.0
FAC B:M3F2 2.2 28.1 1.0
CAN B:M3F2 2.3 21.2 1.0
CAJ B:M3F2 2.8 21.3 1.0
CD1 B:ILE1075 3.0 29.8 1.0
CG2 B:ILE1051 3.4 23.0 0.5
NAK B:M3F2 3.5 17.4 1.0
CB B:TYR1050 3.6 31.1 0.5
CG B:TYR1050 3.8 32.1 0.5
O B:ALA1049 3.8 28.7 0.5
CD2 B:TYR1050 3.9 33.5 0.5
CG1 B:ILE1075 3.9 23.8 1.0
CAM B:M3F2 4.2 21.8 1.0
CA B:TYR1050 4.3 31.1 0.5
CB B:ILE1051 4.3 24.1 0.5
CD1 B:ILE1051 4.4 24.0 0.5
CE2 B:PHE1035 4.6 33.0 1.0
CAQ B:M3F2 4.7 17.3 1.0
CD1 B:TYR1050 4.7 33.4 0.5
C B:ALA1049 4.8 28.4 0.5
O B:HOH13 4.8 16.7 1.0
CE2 B:TYR1050 4.8 34.4 0.5
CG1 B:ILE1051 4.9 24.0 0.5
CD1 B:TYR1071 5.0 18.0 1.0
N B:TYR1050 5.0 30.2 0.5

Reference:

E.Wahlberg, T.Karlberg, E.Kouznetsova, N.Markova, A.Macchiarulo, A.G.Thorsell, E.Pol, A.Frostell, T.Ekblad, B.Kull, G.M.Robertson, R.Pellicciari, H.Schuler, J.Weigelt. Family-Wide Chemical Profiling and Structural Analysis of Parp and Tankyrase Inhibitors Nat.Biotechnol. V. 30 283 2012.
ISSN: ISSN 1087-0156
PubMed: 22343925
DOI: 10.1038/NBT.2121
Page generated: Mon Jul 14 17:54:30 2025

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