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Chlorine in PDB 6e6e: Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase

Enzymatic activity of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase

All present enzymatic activity of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase:
2.7.10.2;

Protein crystallography data

The structure of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase, PDB code: 6e6e was solved by D.Gurbani, A.Bera, K.Westover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.66 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.534, 84.028, 120.109, 89.96, 90.05, 90.12
R / Rfree (%) 25 / 28.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase (pdb code 6e6e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase, PDB code: 6e6e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6e6e

Go back to Chlorine Binding Sites List in 6e6e
Chlorine binding site 1 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:56.4
occ:1.00
CL1 A:HVY601 0.0 56.4 1.0
C30 A:HVY601 1.7 50.9 1.0
C29 A:HVY601 2.7 46.2 1.0
C25 A:HVY601 2.7 45.9 1.0
N9 A:HVY601 3.0 45.3 1.0
C24 A:HVY601 3.2 42.0 1.0
O3 A:HVY601 3.2 41.4 1.0
CG1 A:VAL323 3.5 33.5 1.0
O A:HOH701 3.5 46.9 1.0
CB A:ALA403 3.5 29.8 1.0
CD1 A:LEU393 3.6 33.9 1.0
CB A:VAL323 3.7 42.2 1.0
CG2 A:VAL323 3.7 33.3 1.0
C28 A:HVY601 4.0 46.1 1.0
C26 A:HVY601 4.0 47.1 1.0
C13 A:HVY601 4.2 38.1 1.0
CA A:ALA403 4.5 32.6 1.0
C27 A:HVY601 4.5 46.7 1.0
C22 A:HVY601 4.5 42.8 1.0
OG1 A:THR338 4.6 41.4 1.0
N A:ASP404 4.8 40.7 1.0
C12 A:HVY601 4.8 41.3 1.0
CG A:LEU393 4.8 31.1 1.0

Chlorine binding site 2 out of 8 in 6e6e

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Chlorine binding site 2 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:54.4
occ:1.00
CL1 B:HVY601 0.0 54.4 1.0
C30 B:HVY601 1.7 51.1 1.0
C29 B:HVY601 2.7 44.4 1.0
C25 B:HVY601 2.7 46.4 1.0
N9 B:HVY601 3.0 41.4 1.0
C24 B:HVY601 3.3 43.2 1.0
O3 B:HVY601 3.3 43.6 1.0
CG1 B:VAL323 3.4 39.5 1.0
CB B:ALA403 3.5 36.7 1.0
CB B:VAL323 3.7 40.7 1.0
O B:HOH709 3.7 49.7 1.0
CG2 B:VAL323 3.8 34.7 1.0
CD1 B:LEU393 3.8 35.6 1.0
C28 B:HVY601 4.0 44.1 1.0
C26 B:HVY601 4.0 49.2 1.0
C13 B:HVY601 4.2 38.3 1.0
CA B:ALA403 4.3 35.5 1.0
C27 B:HVY601 4.5 48.2 1.0
N B:ASP404 4.6 44.0 1.0
OG1 B:THR338 4.6 43.1 1.0
C12 B:HVY601 4.7 38.0 1.0
C22 B:HVY601 4.9 42.8 1.0
C23 B:HVY601 4.9 56.2 1.0
CG B:LEU393 5.0 33.2 1.0

Chlorine binding site 3 out of 8 in 6e6e

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Chlorine binding site 3 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:52.8
occ:1.00
CL1 C:HVY601 0.0 52.8 1.0
C30 C:HVY601 1.7 48.0 1.0
C29 C:HVY601 2.7 47.1 1.0
C25 C:HVY601 2.7 42.5 1.0
N9 C:HVY601 3.0 38.6 1.0
C24 C:HVY601 3.2 40.2 1.0
O3 C:HVY601 3.3 41.9 1.0
CB C:ALA403 3.5 35.2 1.0
CG1 C:VAL323 3.5 36.2 1.0
CD1 C:LEU393 3.6 36.4 1.0
CB C:VAL323 3.8 37.8 1.0
CG2 C:VAL323 4.0 33.1 1.0
C28 C:HVY601 4.0 46.8 1.0
C26 C:HVY601 4.0 42.3 1.0
O C:HOH722 4.1 46.9 1.0
C13 C:HVY601 4.2 38.9 1.0
CA C:ALA403 4.5 39.7 1.0
C27 C:HVY601 4.5 43.3 1.0
OG1 C:THR338 4.6 43.8 1.0
C22 C:HVY601 4.7 39.2 1.0
C12 C:HVY601 4.8 37.1 1.0
N C:ASP404 4.8 44.3 1.0
CG C:LEU393 4.8 33.2 1.0

Chlorine binding site 4 out of 8 in 6e6e

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Chlorine binding site 4 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:55.0
occ:1.00
CL1 D:HVY601 0.0 55.0 1.0
C30 D:HVY601 1.7 49.6 1.0
C29 D:HVY601 2.7 50.6 1.0
C25 D:HVY601 2.7 39.8 1.0
N9 D:HVY601 3.0 33.1 1.0
C24 D:HVY601 3.2 39.1 1.0
O3 D:HVY601 3.3 42.3 1.0
CG1 D:VAL323 3.5 40.1 1.0
CB D:ALA403 3.5 39.7 1.0
CD1 D:LEU393 3.7 33.1 1.0
CB D:VAL323 3.8 38.9 1.0
CG2 D:VAL323 3.9 36.6 1.0
C28 D:HVY601 4.0 49.7 1.0
C26 D:HVY601 4.0 47.8 1.0
C13 D:HVY601 4.2 40.3 1.0
CA D:ALA403 4.4 44.2 1.0
C27 D:HVY601 4.5 49.0 1.0
OG1 D:THR338 4.6 41.4 1.0
N D:ASP404 4.6 45.5 1.0
C22 D:HVY601 4.8 44.4 1.0
C12 D:HVY601 4.8 38.9 1.0
CG D:LEU393 5.0 29.8 1.0

Chlorine binding site 5 out of 8 in 6e6e

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Chlorine binding site 5 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl601

b:53.4
occ:1.00
CL1 E:HVY601 0.0 53.4 1.0
C30 E:HVY601 1.7 47.4 1.0
C29 E:HVY601 2.7 42.6 1.0
C25 E:HVY601 2.7 44.8 1.0
N9 E:HVY601 2.9 44.1 1.0
O E:ALA293 3.3 48.3 1.0
OG1 E:THR338 3.4 46.1 1.0
C24 E:HVY601 3.5 44.1 1.0
N E:LYS295 3.5 46.8 1.0
O E:ILE336 3.6 48.1 1.0
CB E:LYS295 3.7 50.9 1.0
C E:ALA293 3.7 45.0 1.0
O3 E:HVY601 3.8 41.5 1.0
C E:ILE294 4.0 48.3 1.0
C28 E:HVY601 4.0 46.4 1.0
C26 E:HVY601 4.0 44.9 1.0
CB E:ALA293 4.0 41.9 1.0
N E:ILE294 4.1 49.4 1.0
CA E:LYS295 4.1 53.9 1.0
CA E:ILE294 4.2 43.8 1.0
CG2 E:THR338 4.2 47.8 1.0
C13 E:HVY601 4.3 40.9 1.0
N E:THR338 4.3 51.9 1.0
CB E:THR338 4.4 44.9 1.0
CG1 E:VAL281 4.4 46.8 1.0
O E:HOH711 4.5 48.8 1.0
C27 E:HVY601 4.5 50.2 1.0
CA E:ALA293 4.5 47.6 1.0
C E:ILE336 4.6 48.6 1.0
C12 E:HVY601 4.6 45.6 1.0
O E:ILE294 4.8 49.0 1.0
CA E:THR338 4.9 50.2 1.0
CA E:VAL337 5.0 50.2 1.0
C E:VAL337 5.0 50.7 1.0

Chlorine binding site 6 out of 8 in 6e6e

Go back to Chlorine Binding Sites List in 6e6e
Chlorine binding site 6 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl601

b:56.8
occ:1.00
CL1 F:HVY601 0.0 56.8 1.0
C30 F:HVY601 1.7 46.1 1.0
C29 F:HVY601 2.7 46.3 1.0
C25 F:HVY601 2.7 45.0 1.0
N9 F:HVY601 3.0 41.3 1.0
O3 F:HVY601 3.2 35.6 1.0
C24 F:HVY601 3.2 41.2 1.0
CD1 F:LEU393 3.5 26.4 1.0
CG1 F:VAL323 3.6 34.0 1.0
CB F:ALA403 3.6 37.6 1.0
CG2 F:VAL323 3.8 32.2 1.0
O F:HOH711 3.8 42.1 1.0
CB F:VAL323 3.8 40.1 1.0
C28 F:HVY601 4.0 44.2 1.0
C26 F:HVY601 4.0 41.2 1.0
C13 F:HVY601 4.2 39.7 1.0
C23 F:HVY601 4.3 59.5 1.0
C22 F:HVY601 4.4 48.1 1.0
C27 F:HVY601 4.5 44.6 1.0
OG1 F:THR338 4.6 45.2 1.0
CA F:ALA403 4.6 41.7 1.0
CG F:LEU393 4.8 34.0 1.0
C12 F:HVY601 4.8 42.6 1.0
N F:ASP404 4.9 45.1 1.0

Chlorine binding site 7 out of 8 in 6e6e

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Chlorine binding site 7 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl601

b:58.9
occ:1.00
CL1 G:HVY601 0.0 58.9 1.0
C30 G:HVY601 1.7 38.4 1.0
C25 G:HVY601 2.7 39.4 1.0
C29 G:HVY601 2.7 47.8 1.0
N9 G:HVY601 2.9 37.4 1.0
OG1 G:THR338 3.3 47.0 1.0
C24 G:HVY601 3.5 40.5 1.0
O G:ALA293 3.5 45.0 1.0
CB G:LYS295 3.6 52.8 1.0
C G:ALA293 3.7 47.8 1.0
O G:ILE336 3.8 54.4 1.0
O3 G:HVY601 3.8 40.9 1.0
CB G:ALA293 3.8 46.0 1.0
N G:LYS295 3.8 49.8 1.0
C G:ILE294 4.0 51.6 1.0
C28 G:HVY601 4.0 50.2 1.0
C26 G:HVY601 4.0 43.1 1.0
N G:ILE294 4.1 41.5 1.0
CG2 G:THR338 4.2 46.6 1.0
CA G:LYS295 4.2 49.7 1.0
C13 G:HVY601 4.3 44.6 1.0
CA G:ILE294 4.3 49.3 1.0
CB G:THR338 4.3 46.7 1.0
CG1 G:VAL281 4.3 44.6 1.0
CA G:ALA293 4.4 52.5 1.0
N G:THR338 4.4 54.4 1.0
O G:ILE294 4.5 50.6 1.0
C27 G:HVY601 4.5 49.5 1.0
C12 G:HVY601 4.5 42.2 1.0
O G:HOH704 4.5 47.1 1.0
CG G:LYS295 4.6 58.3 1.0
C G:ILE336 4.7 54.4 1.0
CD G:LYS295 4.9 51.9 1.0
CA G:THR338 5.0 51.1 1.0
CG2 G:VAL281 5.0 49.0 1.0

Chlorine binding site 8 out of 8 in 6e6e

Go back to Chlorine Binding Sites List in 6e6e
Chlorine binding site 8 out of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl601

b:60.1
occ:1.00
CL1 H:HVY601 0.0 60.1 1.0
C30 H:HVY601 1.7 49.5 1.0
C29 H:HVY601 2.7 49.5 1.0
C25 H:HVY601 2.7 47.9 1.0
N9 H:HVY601 3.0 41.5 1.0
O3 H:HVY601 3.2 37.6 1.0
C24 H:HVY601 3.2 38.1 1.0
CD1 H:LEU393 3.4 29.8 1.0
O H:HOH706 3.5 46.1 1.0
CG1 H:VAL323 3.6 32.1 1.0
CB H:ALA403 3.6 34.8 1.0
CB H:VAL323 3.9 45.7 1.0
CG2 H:VAL323 3.9 37.4 1.0
C28 H:HVY601 4.0 47.5 1.0
C26 H:HVY601 4.0 44.8 1.0
C13 H:HVY601 4.2 38.5 1.0
C27 H:HVY601 4.5 43.8 1.0
C22 H:HVY601 4.5 36.2 1.0
CG H:LEU393 4.7 30.9 1.0
CA H:ALA403 4.7 35.9 1.0
OG1 H:THR338 4.7 40.2 1.0
C12 H:HVY601 4.8 39.2 1.0
N H:ASP404 4.8 41.5 1.0

Reference:

D.Gurbani, A.K.Bera, K.Westover. Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase To Be Published.
Page generated: Sat Jul 12 13:16:39 2025

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