Fluorine in PDB 5sys: C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor

Enzymatic activity of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor

All present enzymatic activity of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor:
2.7.10.2;

Protein crystallography data

The structure of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor, PDB code: 5sys was solved by E.M.Dieter, E.A.Merritt, D.J.Maly, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.94 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.813, 63.857, 75.625, 77.87, 90.10, 89.83
R / Rfree (%) 28.6 / 33.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor (pdb code 5sys). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor, PDB code: 5sys:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 1 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:75.4
occ:1.00
 F A:72F600 0.0 75.4 1.0
C17 A:72F600 1.3 70.5 1.0
F2 A:72F600 2.1 66.3 1.0
F1 A:72F600 2.1 71.0 1.0
C16 A:72F600 2.3 69.7 1.0
C15 A:72F600 3.0 69.8 1.0
CD2 A:HIS384 3.2 59.5 1.0
NE2 A:HIS384 3.4 61.2 1.0
C18 A:72F600 3.4 69.3 1.0
CG1 A:VAL402 3.6 51.8 1.0
O A:ALA403 3.9 59.3 1.0
O A:VAL402 4.2 53.3 1.0
C A:ALA403 4.2 59.8 1.0
C14 A:72F600 4.3 75.4 1.0
CB A:VAL402 4.3 52.1 1.0
C A:VAL402 4.4 54.7 1.0
CG A:HIS384 4.4 60.8 1.0
N A:ALA403 4.5 56.9 1.0
C19 A:72F600 4.6 69.8 1.0
CA A:ALA403 4.6 60.2 1.0
CE1 A:HIS384 4.6 62.2 1.0
CB A:ASP404 4.6 73.0 1.0
CG A:LEU322 4.8 61.5 1.0
N A:ASP404 4.9 63.4 1.0
C20 A:72F600 4.9 72.6 1.0

Fluorine binding site 2 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 2 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:71.0
occ:1.00
 F1 A:72F600 0.0 71.0 1.0
C17 A:72F600 1.3 70.5 1.0
F A:72F600 2.1 75.4 1.0
F2 A:72F600 2.1 66.3 1.0
C16 A:72F600 2.4 69.7 1.0
C18 A:72F600 2.7 69.3 1.0
CD1 A:LEU317 3.6 73.0 1.0
C15 A:72F600 3.6 69.8 1.0
C19 A:72F600 4.1 69.8 1.0
CD2 A:HIS384 4.4 59.5 1.0
CG1 A:VAL313 4.5 82.1 1.0
C14 A:72F600 4.8 75.4 1.0
CD2 A:LEU322 4.8 61.3 1.0
NE2 A:HIS384 4.9 61.2 1.0
C20 A:72F600 5.0 72.6 1.0

Fluorine binding site 3 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 3 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:66.3
occ:1.00
 F2 A:72F600 0.0 66.3 1.0
C17 A:72F600 1.3 70.5 1.0
F A:72F600 2.1 75.4 1.0
F1 A:72F600 2.1 71.0 1.0
C16 A:72F600 2.3 69.7 1.0
C15 A:72F600 2.9 69.8 1.0
C18 A:72F600 3.5 69.3 1.0
CG A:LEU322 3.6 61.5 1.0
CD2 A:LEU322 3.6 61.3 1.0
CD1 A:LEU317 4.0 73.0 1.0
C14 A:72F600 4.2 75.4 1.0
O A:VAL402 4.3 53.3 1.0
CB A:LEU322 4.4 59.2 1.0
C19 A:72F600 4.6 69.8 1.0
CD1 A:LEU322 4.7 62.8 1.0
C20 A:72F600 4.9 72.6 1.0

Fluorine binding site 4 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 4 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:63.2
occ:1.00
 F B:72F600 0.0 63.2 1.0
C17 B:72F600 1.3 67.6 1.0
F1 B:72F600 2.1 62.8 1.0
F2 B:72F600 2.2 67.1 1.0
C16 B:72F600 2.3 71.2 1.0
C15 B:72F600 2.9 70.8 1.0
C18 B:72F600 3.5 74.0 1.0
O B:VAL402 3.6 49.9 1.0
O B:ALA403 3.8 61.6 1.0
CG1 B:VAL402 3.9 58.4 1.0
C B:ALA403 3.9 57.0 1.0
NE2 B:HIS384 3.9 53.9 1.0
C B:VAL402 4.0 53.3 1.0
CD2 B:HIS384 4.0 51.8 1.0
CA B:ALA403 4.1 54.6 1.0
N B:ALA403 4.2 52.4 1.0
C14 B:72F600 4.2 74.3 1.0
CB B:VAL402 4.4 56.6 1.0
N B:ASP404 4.5 61.2 1.0
CG B:LEU322 4.6 59.6 1.0
CB B:ASP404 4.6 67.0 1.0
C19 B:72F600 4.6 74.7 1.0
CA B:VAL402 4.9 54.9 1.0
C20 B:72F600 4.9 75.0 1.0
CD2 B:LEU322 5.0 60.0 1.0

Fluorine binding site 5 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 5 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:62.8
occ:1.00
 F1 B:72F600 0.0 62.8 1.0
C17 B:72F600 1.3 67.6 1.0
F B:72F600 2.1 63.2 1.0
F2 B:72F600 2.1 67.1 1.0
C16 B:72F600 2.4 71.2 1.0
C18 B:72F600 2.7 74.0 1.0
C15 B:72F600 3.6 70.8 1.0
CD1 B:LEU317 3.8 65.0 1.0
C19 B:72F600 4.1 74.7 1.0
CD2 B:HIS384 4.4 51.8 1.0
NE2 B:HIS384 4.8 53.9 1.0
C14 B:72F600 4.8 74.3 1.0
CG1 B:VAL313 4.9 85.3 1.0
C20 B:72F600 5.0 75.0 1.0

Fluorine binding site 6 out of 6 in 5sys

Go back to Fluorine Binding Sites List in 5sys
Fluorine binding site 6 out of 6 in the C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of C-Src V281C Bound to N-[3-({6-[(1E)-2-Cyano-3-(Methylamino)-3-Oxoprop- 1-En-1-Yl]-7-(2-Methoxyethyl)-7H-Pyrrolo[2,3-D]Pyrimidin-5- Yl}Ethynyl)-4-Methylphenyl]-3-(Trifluoromethyl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:67.1
occ:1.00
 F2 B:72F600 0.0 67.1 1.0
C17 B:72F600 1.3 67.6 1.0
F1 B:72F600 2.1 62.8 1.0
F B:72F600 2.2 63.2 1.0
C16 B:72F600 2.4 71.2 1.0
C15 B:72F600 3.1 70.8 1.0
C18 B:72F600 3.4 74.0 1.0
CD1 B:LEU317 3.7 65.0 1.0
CD2 B:LEU322 4.0 60.0 1.0
CG B:LEU322 4.1 59.6 1.0
C14 B:72F600 4.4 74.3 1.0
C19 B:72F600 4.6 74.7 1.0
O B:VAL402 4.6 49.9 1.0
CB B:LEU322 4.7 57.7 1.0
CB B:LEU317 4.8 66.5 1.0
CG B:MET314 4.9 57.8 1.0
CG B:LEU317 4.9 65.0 1.0
C20 B:72F600 5.0 75.0 1.0

Reference:

A.C.Register, D.J.Maly. A Combined Approach Reveals A Regulatory Mechanism Coupling Src'S Kinase Activity, Localization, and Phosphotransferase-Independent Functions Mol.Cell V.2019.
ISSN: ISSN 1097-2765
Page generated: Sun Dec 13 12:37:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy