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Fluorine in PDB 6b8y: Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine

Enzymatic activity of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine

All present enzymatic activity of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine:
2.7.11.30;

Protein crystallography data

The structure of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine, PDB code: 6b8y was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.92 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.110, 77.030, 90.440, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine (pdb code 6b8y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine, PDB code: 6b8y:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6b8y

Go back to Fluorine Binding Sites List in 6b8y
Fluorine binding site 1 out of 4 in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:15.9
occ:1.00
 F18 A:D0A601 0.0 15.9 1.0
C17 A:D0A601 1.4 15.0 1.0
H31 A:D0A601 2.3 14.6 0.0
C12 A:D0A601 2.4 13.6 1.0
C16 A:D0A601 2.4 14.3 1.0
H34 A:D0A601 2.7 14.4 0.0
N10 A:D0A601 2.7 14.5 1.0
O A:HOH854 2.9 17.7 1.0
O A:HOH797 3.2 21.0 1.0
CG2 A:ILE211 3.4 23.9 1.0
CA A:GLY286 3.5 15.5 1.0
C13 A:D0A601 3.6 12.2 1.0
N15 A:D0A601 3.6 15.2 1.0
O A:HOH892 3.8 25.1 1.0
O A:HOH868 3.9 27.4 1.0
C6 A:D0A601 4.1 13.9 1.0
C14 A:D0A601 4.1 12.8 1.0
CD2 A:LEU340 4.1 21.2 1.0
C A:GLY286 4.2 16.4 1.0
N A:SER287 4.3 15.5 1.0
CD1 A:ILE211 4.5 23.9 1.0
H32 A:D0A601 4.5 12.2 0.0
N A:GLY286 4.6 16.6 1.0
H28 A:D0A601 4.6 13.7 0.0
O A:HIS283 4.7 15.7 1.0
CB A:ILE211 4.7 22.6 1.0
O A:HOH888 4.8 29.1 1.0
N5 A:D0A601 4.9 11.4 1.0
C1 A:D0A601 4.9 12.9 1.0

Fluorine binding site 2 out of 4 in 6b8y

Go back to Fluorine Binding Sites List in 6b8y
Fluorine binding site 2 out of 4 in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:16.7
occ:1.00
 F25 A:D0A601 0.0 16.7 1.0
C24 A:D0A601 1.3 16.7 1.0
F26 A:D0A601 2.1 17.1 1.0
F27 A:D0A601 2.2 15.6 1.0
C22 A:D0A601 2.4 14.8 1.0
N23 A:D0A601 2.8 13.7 1.0
O A:HOH735 3.2 15.2 1.0
CD A:GLU245 3.2 18.1 1.0
OE2 A:GLU245 3.3 18.1 1.0
CE2 A:TYR249 3.4 14.3 1.0
CD1 A:LEU278 3.4 13.8 1.0
C21 A:D0A601 3.5 14.7 1.0
OE1 A:GLU245 3.6 23.7 1.0
CG A:GLU245 3.6 15.1 1.0
CD2 A:TYR249 3.7 13.8 1.0
H37 A:D0A601 3.8 14.8 0.0
CE A:LYS232 3.9 24.0 1.0
CB A:LEU278 4.0 10.9 1.0
CZ A:TYR249 4.1 15.9 1.0
C11 A:D0A601 4.1 12.7 1.0
NZ A:LYS232 4.2 20.9 1.0
CG A:LEU278 4.3 13.7 1.0
OH A:TYR249 4.4 18.5 1.0
C20 A:D0A601 4.7 12.6 1.0
CB A:GLU245 4.7 12.1 1.0
CG A:TYR249 4.7 13.2 1.0
CD1 A:PHE262 4.9 18.4 1.0
C19 A:D0A601 4.9 11.1 1.0
CD A:LYS232 5.0 21.1 1.0

Fluorine binding site 3 out of 4 in 6b8y

Go back to Fluorine Binding Sites List in 6b8y
Fluorine binding site 3 out of 4 in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:17.1
occ:1.00
 F26 A:D0A601 0.0 17.1 1.0
C24 A:D0A601 1.3 16.7 1.0
F25 A:D0A601 2.1 16.7 1.0
F27 A:D0A601 2.1 15.6 1.0
C22 A:D0A601 2.3 14.8 1.0
N23 A:D0A601 2.8 13.7 1.0
CE2 A:TYR249 3.0 14.3 1.0
CZ A:TYR249 3.1 15.9 1.0
O A:HOH735 3.2 15.2 1.0
OH A:TYR249 3.3 18.5 1.0
C21 A:D0A601 3.4 14.7 1.0
CD2 A:TYR249 3.5 13.8 1.0
H37 A:D0A601 3.7 14.8 0.0
CE1 A:TYR249 3.7 15.7 1.0
CD2 A:LEU260 3.7 15.9 1.0
C11 A:D0A601 4.0 12.7 1.0
CG A:TYR249 4.1 13.2 1.0
CD1 A:TYR249 4.2 13.9 1.0
CB A:SER280 4.2 12.6 1.0
CD1 A:PHE262 4.3 18.4 1.0
CG A:LEU260 4.4 14.2 1.0
C20 A:D0A601 4.5 12.6 1.0
OE2 A:GLU245 4.5 18.1 1.0
OG A:SER280 4.7 13.4 1.0
C19 A:D0A601 4.8 11.1 1.0
CD A:GLU245 4.9 18.1 1.0
CB A:LEU260 5.0 11.8 1.0

Fluorine binding site 4 out of 4 in 6b8y

Go back to Fluorine Binding Sites List in 6b8y
Fluorine binding site 4 out of 4 in the Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Tgf-Beta Receptor Type 1 Kinase Domain (T204D) in Complex with N-(3- Fluoropyridin-4-Yl)-2-[6-(Trifluoromethyl)Pyridin-2-Yl]-7H-Pyrrolo[2, 3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:15.6
occ:1.00
 F27 A:D0A601 0.0 15.6 1.0
C24 A:D0A601 1.3 16.7 1.0
F26 A:D0A601 2.1 17.1 1.0
F25 A:D0A601 2.2 16.7 1.0
C22 A:D0A601 2.4 14.8 1.0
H37 A:D0A601 2.5 14.8 0.0
C21 A:D0A601 2.8 14.7 1.0
CB A:LEU278 3.3 10.9 1.0
CD1 A:PHE262 3.3 18.4 1.0
N23 A:D0A601 3.6 13.7 1.0
CE1 A:PHE262 3.6 18.2 1.0
CD1 A:LEU278 4.0 13.8 1.0
O A:VAL279 4.1 11.9 1.0
C20 A:D0A601 4.1 12.6 1.0
CG A:LEU278 4.1 13.7 1.0
C A:LEU278 4.2 13.5 1.0
N A:VAL279 4.2 11.1 1.0
CA A:LEU278 4.2 10.8 1.0
CD2 A:TYR249 4.2 13.8 1.0
CE2 A:TYR249 4.3 14.3 1.0
C A:VAL279 4.3 12.0 1.0
CB A:SER280 4.4 12.6 1.0
CG A:PHE262 4.5 15.3 1.0
O A:LEU278 4.6 12.4 1.0
CD2 A:LEU278 4.6 14.7 1.0
C11 A:D0A601 4.7 12.7 1.0
CG A:TYR249 4.7 13.2 1.0
H36 A:D0A601 4.8 12.7 0.0
CZ A:TYR249 4.8 15.9 1.0
N A:SER280 4.8 10.9 1.0
CA A:VAL279 4.8 10.6 1.0
O A:HOH735 4.8 15.2 1.0
C19 A:D0A601 4.9 11.1 1.0
CZ A:PHE262 4.9 17.5 1.0
CB A:PHE262 5.0 14.8 1.0

Reference:

L.S.Harikrishnan, J.Warrier, A.J.Tebben, G.Tonukunuru, S.R.Madduri, V.Baligar, R.Mannoori, B.Seshadri, H.Rahaman, P.N.Arunachalam, A.G.Dikundwar, B.E.Fink, J.Fargnoli, M.Fereshteh, Y.Fan, J.Lippy, C.P.Ho, B.Wautlet, S.Sheriff, M.Ruzanov, R.M.Borzilleri. Heterobicyclic Inhibitors of Transforming Growth Factor Beta Receptor I (Tgf Beta Ri). Bioorg. Med. Chem. V. 26 1026 2018.
ISSN: ESSN 1464-3391
PubMed: 29422332
DOI: 10.1016/J.BMC.2018.01.014
Page generated: Thu Aug 1 17:59:55 2024

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