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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

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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

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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

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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

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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: Thu Aug 1 14:59:44 2024

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