Atomistry » Fluorine » PDB 3syn-3u2o » 3tud
Atomistry »
  Fluorine »
    PDB 3syn-3u2o »
      3tud »

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: Wed Jul 31 22:47:43 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