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Fluorine in PDB 3tud: Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide

Enzymatic activity of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide, PDB code: 3tud was solved by F.Lovering, J.Mcdonald, G.Whitlock, P.Glossop, C.Phillips, Y.Sabnis, M.Ryan, L.Fitz, J.Lee, J.S.Chang, S.Han, R.Kurumbail, A.Thorarenson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.58 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.799, 68.066, 82.790, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 26.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide (pdb code 3tud). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide, PDB code: 3tud:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3tud

Go back to Fluorine Binding Sites List in 3tud
Fluorine binding site 1 out of 3 in the Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:62.4
occ:1.00
 F16 A:FPX1 0.0 62.4 1.0
C15 A:FPX1 1.4 59.1 1.0
F18 A:FPX1 2.2 57.1 1.0
F17 A:FPX1 2.3 59.4 1.0
C13 A:FPX1 2.4 58.9 1.0
C12 A:FPX1 3.0 59.7 1.0
CD2 A:HIS492 3.4 48.9 1.0
C14 A:FPX1 3.5 58.0 1.0
CD1 A:LEU485 3.6 49.6 1.0
CE2 A:PHE490 3.8 60.9 1.0
NE2 A:HIS492 3.9 49.0 1.0
CG2 A:ILE510 4.2 45.2 1.0
CD2 A:LEU485 4.2 51.9 1.0
CG A:HIS492 4.3 46.9 1.0
CD2 A:PHE490 4.4 58.8 1.0
C11 A:FPX1 4.4 59.6 1.0
CB A:ASP512 4.4 56.6 1.0
CG A:LEU485 4.6 49.6 1.0
CZ A:PHE490 4.6 58.5 1.0
O A:SER511 4.7 51.4 1.0
C9 A:FPX1 4.7 58.7 1.0
OD1 A:ASP512 4.8 74.2 1.0
CE1 A:HIS492 4.8 48.5 1.0
CB A:HIS492 4.9 43.8 1.0
C A:SER511 4.9 51.3 1.0

Fluorine binding site 2 out of 3 in 3tud

Go back to Fluorine Binding Sites List in 3tud
Fluorine binding site 2 out of 3 in the Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:59.4
occ:1.00
 F17 A:FPX1 0.0 59.4 1.0
C15 A:FPX1 1.4 59.1 1.0
F18 A:FPX1 2.1 57.1 1.0
F16 A:FPX1 2.3 62.4 1.0
C13 A:FPX1 2.4 58.9 1.0
C14 A:FPX1 2.7 58.0 1.0
O A:ILE510 3.1 46.0 1.0
C12 A:FPX1 3.7 59.7 1.0
CG1 A:ILE432 3.7 50.1 1.0
C A:ILE510 3.8 45.9 1.0
CG2 A:ILE432 3.9 48.8 1.0
CG2 A:ILE510 4.0 45.2 1.0
C9 A:FPX1 4.1 58.7 1.0
CB A:ILE432 4.1 49.6 1.0
CA A:SER511 4.2 43.6 1.0
N A:SER511 4.3 42.3 1.0
CB A:ILE510 4.3 46.5 1.0
C A:SER511 4.4 51.3 1.0
O8 A:FPX1 4.5 62.4 1.0
O A:SER511 4.6 51.4 1.0
CA A:ILE432 4.6 45.8 1.0
N A:VAL433 4.6 50.4 1.0
CE A:MET424 4.6 66.8 1.0
CA A:ILE510 4.7 43.9 1.0
CD1 A:LEU485 4.7 49.6 1.0
C11 A:FPX1 4.9 59.6 1.0
N A:ASP512 4.9 51.4 1.0
C7 A:FPX1 4.9 61.3 1.0
CD2 A:LEU485 4.9 51.9 1.0
CD2 A:HIS492 4.9 48.9 1.0

Fluorine binding site 3 out of 3 in 3tud

Go back to Fluorine Binding Sites List in 3tud
Fluorine binding site 3 out of 3 in the Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Syk Kinase Domain with N-(4-Methyl-3-(8-Methyl-7- Oxo-2-(Phenylamino)-7,8-Dihydropyrido[2,3-D]Pyrimidin-6-Yl)Phenyl)-3- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:57.1
occ:1.00
 F18 A:FPX1 0.0 57.1 1.0
C15 A:FPX1 1.4 59.1 1.0
F17 A:FPX1 2.1 59.4 1.0
F16 A:FPX1 2.2 62.4 1.0
C13 A:FPX1 2.3 58.9 1.0
C12 A:FPX1 2.9 59.7 1.0
CD1 A:LEU427 3.3 69.5 1.0
C14 A:FPX1 3.3 58.0 1.0
CD2 A:LEU485 3.6 51.9 1.0
CG2 A:ILE432 4.1 48.8 1.0
CE A:MET424 4.1 66.8 1.0
CG1 A:ILE432 4.2 50.1 1.0
C11 A:FPX1 4.2 59.6 1.0
SD A:MET424 4.3 71.2 1.0
CE2 A:PHE490 4.3 60.9 1.0
CD1 A:LEU485 4.3 49.6 1.0
C9 A:FPX1 4.5 58.7 1.0
CG A:LEU427 4.5 70.6 1.0
CG A:LEU485 4.6 49.6 1.0
CD2 A:PHE490 4.7 58.8 1.0
CB A:ILE432 4.7 49.6 1.0
CB A:LEU427 4.7 66.8 1.0
CZ A:PHE490 4.8 58.5 1.0
C10 A:FPX1 4.9 58.9 1.0

Reference:

F.Lovering, J.Mcdonald, G.A.Whitlock, P.A.Glossop, C.Phillips, A.Bent, Y.Sabnis, M.Ryan, L.Fitz, J.Lee, J.S.Chang, S.Han, R.Kurumbail, A.Thorarensen. Identification of Type-II Inhibitors Using Kinase Structures. Chem.Biol.Drug Des. V. 80 657 2012.
ISSN: ISSN 1747-0277
PubMed: 22759374
DOI: 10.1111/J.1747-0285.2012.01443.X
Page generated: Mon Jul 14 19:30:40 2025

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