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Chlorine in PDB 5h2u: Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib

Enzymatic activity of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib

All present enzymatic activity of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib, PDB code: 5h2u was solved by M.K.Thakur, S.Birudukota, S.Swaminathan, R.Tyagi, R.Gosu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.52 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.881, 77.018, 87.413, 81.36, 75.76, 74.92
R / Rfree (%) 20.6 / 26

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib (pdb code 5h2u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib, PDB code: 5h2u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5h2u

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Chlorine binding site 1 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:27.9
occ:0.50
CL A:1N1501 0.0 27.9 0.5
C10 A:1N1501 0.2 27.9 0.5
C9 A:1N1501 1.6 28.2 0.5
C5 A:1N1501 1.7 28.1 0.5
C8 A:1N1501 2.6 27.7 0.5
C4 A:1N1501 2.6 28.5 0.5
C6 A:1N1501 2.7 27.6 0.5
C4 A:1N1501 2.7 28.5 0.5
N2 A:1N1501 3.0 29.0 1.0
O A:ALA217 3.1 30.3 1.0
O A:ILE262 3.2 29.3 1.0
C A:ALA217 3.4 31.1 1.0
N A:LYS219 3.6 30.4 1.0
C3 A:1N1501 3.6 30.4 1.0
N A:ILE218 3.7 30.7 1.0
OG1 A:THR264 3.7 26.8 1.0
CB A:ALA217 3.7 31.5 1.0
N A:THR264 3.7 28.1 1.0
CA A:ILE218 3.9 30.4 1.0
C7 A:1N1501 3.9 27.9 0.5
C5 A:1N1501 3.9 28.8 0.5
C7 A:1N1501 3.9 27.7 0.5
C9 A:1N1501 4.0 28.5 0.5
C A:ILE218 4.0 30.2 1.0
O A:1N1501 4.0 30.2 1.0
CG A:LYS219 4.1 30.8 1.0
CG2 A:THR264 4.1 25.6 1.0
CA A:ILE263 4.1 28.5 1.0
CA A:ALA217 4.2 31.3 1.0
C A:ILE262 4.2 29.1 1.0
CB A:LYS219 4.2 30.9 1.0
C A:ILE263 4.3 28.2 1.0
CB A:THR264 4.3 28.1 1.0
C6 A:1N1501 4.4 28.1 0.5
C2 A:1N1501 4.4 30.3 1.0
C8 A:1N1501 4.4 27.9 0.5
CA A:LYS219 4.5 30.5 1.0
N A:ILE263 4.5 28.6 1.0
CA A:THR264 4.6 28.0 1.0
CG1 A:VAL205 4.6 30.9 1.0
CD A:LYS219 4.8 30.4 1.0
C1 A:1N1501 4.8 30.9 1.0
O A:ILE218 4.9 29.3 1.0
N A:ALA217 5.0 31.4 1.0

Chlorine binding site 2 out of 8 in 5h2u

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Chlorine binding site 2 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:28.2
occ:0.50
CL A:1N1501 0.0 28.2 0.5
C10 A:1N1501 0.3 28.2 0.5
C9 A:1N1501 1.7 28.5 0.5
C5 A:1N1501 1.7 28.8 0.5
C4 A:1N1501 2.6 28.5 0.5
C8 A:1N1501 2.7 27.9 0.5
C4 A:1N1501 2.7 28.5 0.5
C6 A:1N1501 2.7 28.1 0.5
N2 A:1N1501 2.9 29.0 1.0
C3 A:1N1501 3.4 30.4 1.0
N A:ASP330 3.4 27.3 1.0
O A:HOH694 3.5 26.9 1.0
O A:1N1501 3.5 30.2 1.0
CA A:GLY329 3.6 27.1 1.0
OD1 A:ASP330 3.6 29.2 1.0
CD2 A:LEU319 3.6 25.4 1.0
O A:HOH645 3.7 42.4 1.0
CD2 A:LEU248 3.7 26.2 1.0
C A:GLY329 3.8 27.1 1.0
C5 A:1N1501 3.9 28.1 0.5
C7 A:1N1501 3.9 27.7 0.5
C9 A:1N1501 4.0 28.2 0.5
C7 A:1N1501 4.0 27.9 0.5
NZ A:LYS219 4.2 32.5 1.0
CA A:ASP330 4.3 27.4 1.0
C2 A:1N1501 4.3 30.3 1.0
C6 A:1N1501 4.4 27.6 0.5
CG A:ASP330 4.5 29.1 1.0
C8 A:1N1501 4.5 27.7 0.5
CB A:ASP330 4.6 27.8 1.0
CG A:LEU319 4.7 27.2 1.0
CG A:LEU248 4.7 26.3 1.0
CB A:LEU248 4.8 26.1 1.0
N A:GLY329 4.9 27.4 1.0
C1 A:1N1501 4.9 30.9 1.0
CG2 A:THR264 4.9 25.6 1.0
O A:GLY329 4.9 26.6 1.0
O A:HOH688 5.0 49.5 1.0

Chlorine binding site 3 out of 8 in 5h2u

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Chlorine binding site 3 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:29.7
occ:0.50
CL B:1N1501 0.0 29.7 0.5
C10 B:1N1501 0.5 30.5 0.5
C5 B:1N1501 1.7 29.7 0.5
C9 B:1N1501 1.8 30.4 0.5
C6 B:1N1501 2.7 29.4 0.5
C4 B:1N1501 2.7 30.1 0.5
C4 B:1N1501 2.7 30.7 0.5
C8 B:1N1501 2.9 30.3 0.5
O B:ALA217 2.9 30.6 1.0
N2 B:1N1501 2.9 30.8 1.0
C B:ALA217 3.2 31.0 1.0
O B:ILE262 3.3 29.0 1.0
N B:LYS219 3.5 30.6 1.0
N B:ILE218 3.5 30.9 1.0
C3 B:1N1501 3.5 32.5 1.0
CB B:ALA217 3.6 31.1 1.0
OG1 B:THR264 3.6 28.7 1.0
CA B:ILE218 3.6 30.3 1.0
C B:ILE218 3.7 30.5 1.0
N B:THR264 3.8 29.2 1.0
O B:1N1501 3.9 32.0 1.0
C7 B:1N1501 4.0 29.9 0.5
C9 B:1N1501 4.0 29.9 0.5
CA B:ALA217 4.0 31.4 1.0
C5 B:1N1501 4.0 30.6 0.5
CG B:LYS219 4.1 29.7 1.0
C7 B:1N1501 4.1 30.6 0.5
CA B:ILE263 4.1 28.6 1.0
C B:ILE262 4.2 28.9 1.0
CB B:LYS219 4.3 30.1 1.0
C2 B:1N1501 4.3 32.2 1.0
CG2 B:THR264 4.3 27.9 1.0
C B:ILE263 4.3 29.0 1.0
CB B:THR264 4.4 29.2 1.0
CA B:LYS219 4.4 30.0 1.0
C8 B:1N1501 4.5 29.8 0.5
N B:ILE263 4.5 28.7 1.0
CG1 B:VAL205 4.5 29.9 1.0
C6 B:1N1501 4.6 30.4 0.5
O B:ILE218 4.6 30.9 1.0
CA B:THR264 4.7 29.3 1.0
C1 B:1N1501 4.8 32.6 1.0
N B:ALA217 4.9 32.0 1.0
CD B:LYS219 4.9 29.4 1.0
O B:THR264 5.0 30.6 1.0

Chlorine binding site 4 out of 8 in 5h2u

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Chlorine binding site 4 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:30.8
occ:0.50
CL B:1N1501 0.0 30.8 0.5
C10 B:1N1501 0.5 29.7 0.5
C5 B:1N1501 1.7 30.6 0.5
C9 B:1N1501 1.9 29.9 0.5
C4 B:1N1501 2.7 30.7 0.5
C6 B:1N1501 2.7 30.4 0.5
C4 B:1N1501 2.7 30.1 0.5
C8 B:1N1501 2.9 29.8 0.5
N2 B:1N1501 2.9 30.8 1.0
C3 B:1N1501 3.3 32.5 1.0
N B:ASP330 3.5 25.5 1.0
O B:1N1501 3.5 32.0 1.0
OD1 B:ASP330 3.6 29.9 1.0
O B:HOH658 3.6 28.3 1.0
CA B:GLY329 3.7 25.6 1.0
CD2 B:LEU248 3.7 28.0 1.0
CD2 B:LEU319 3.8 29.1 1.0
NZ B:LYS219 3.8 31.6 1.0
O B:HOH639 3.9 48.6 1.0
C B:GLY329 4.0 25.4 1.0
C9 B:1N1501 4.0 30.4 0.5
C7 B:1N1501 4.0 30.6 0.5
C5 B:1N1501 4.0 29.7 0.5
C7 B:1N1501 4.1 29.9 0.5
C2 B:1N1501 4.3 32.2 1.0
CA B:ASP330 4.3 25.9 1.0
CG B:ASP330 4.5 28.4 1.0
C8 B:1N1501 4.5 30.3 0.5
C6 B:1N1501 4.6 29.4 0.5
CG B:LEU248 4.6 28.6 1.0
CB B:ASP330 4.7 26.1 1.0
CG B:LEU319 4.7 28.1 1.0
CB B:LEU248 4.8 28.0 1.0
C1 B:1N1501 4.8 32.6 1.0
CG2 B:THR264 4.9 27.9 1.0
N B:GLY329 5.0 26.1 1.0

Chlorine binding site 5 out of 8 in 5h2u

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Chlorine binding site 5 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:32.0
occ:0.50
CL C:1N1501 0.0 32.0 0.5
C10 C:1N1501 0.4 30.6 0.5
C5 C:1N1501 1.7 31.4 0.5
C9 C:1N1501 1.7 30.3 0.5
C4 C:1N1501 2.6 31.1 0.5
C4 C:1N1501 2.7 32.0 0.5
C6 C:1N1501 2.7 31.4 0.5
C8 C:1N1501 2.8 30.1 0.5
N2 C:1N1501 2.9 32.5 1.0
O C:ALA217 2.9 32.0 1.0
C C:ALA217 3.3 32.5 1.0
O C:ILE262 3.4 29.5 1.0
N C:LYS219 3.6 30.4 1.0
C3 C:1N1501 3.6 35.3 1.0
N C:ILE218 3.7 31.8 1.0
CB C:ALA217 3.7 33.2 1.0
OG1 C:THR264 3.8 29.4 1.0
N C:THR264 3.8 29.3 1.0
CG C:LYS219 3.8 28.3 1.0
CA C:ILE218 3.9 31.2 1.0
C5 C:1N1501 3.9 30.5 0.5
C C:ILE218 3.9 31.0 1.0
C9 C:1N1501 3.9 31.7 0.5
C7 C:1N1501 4.0 31.5 0.5
C7 C:1N1501 4.0 30.4 0.5
CA C:ILE263 4.1 29.3 1.0
CA C:ALA217 4.1 32.8 1.0
O C:1N1501 4.2 34.9 1.0
CB C:LYS219 4.2 29.8 1.0
C C:ILE262 4.3 29.7 1.0
C C:ILE263 4.3 29.1 1.0
CG2 C:THR264 4.3 27.3 1.0
C2 C:1N1501 4.4 36.1 1.0
C8 C:1N1501 4.4 31.4 0.5
CA C:LYS219 4.5 30.0 1.0
CB C:THR264 4.5 29.8 1.0
C6 C:1N1501 4.5 30.1 0.5
N C:ILE263 4.6 29.7 1.0
CD C:LYS219 4.7 26.6 1.0
CA C:THR264 4.7 29.8 1.0
O C:ILE218 4.8 30.9 1.0
CE C:LYS219 4.8 26.8 1.0
C1 C:1N1501 4.9 36.5 1.0
CG1 C:VAL205 4.9 35.8 1.0
O C:THR264 4.9 31.3 1.0
N C:ALA217 5.0 33.5 1.0

Chlorine binding site 6 out of 8 in 5h2u

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Chlorine binding site 6 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:30.1
occ:0.50
CL C:1N1501 0.0 30.1 0.5
C10 C:1N1501 0.4 31.6 0.5
C5 C:1N1501 1.7 30.5 0.5
C9 C:1N1501 1.7 31.7 0.5
C4 C:1N1501 2.6 32.0 0.5
C4 C:1N1501 2.7 31.1 0.5
C6 C:1N1501 2.7 30.1 0.5
C8 C:1N1501 2.8 31.4 0.5
N2 C:1N1501 2.9 32.5 1.0
C3 C:1N1501 3.1 35.3 1.0
O C:1N1501 3.2 34.9 1.0
N C:ASP330 3.6 31.6 1.0
O C:HOH669 3.7 28.7 1.0
OD1 C:ASP330 3.7 33.5 1.0
CA C:GLY329 3.8 31.1 1.0
CD2 C:LEU248 3.8 32.7 1.0
CD2 C:LEU319 3.9 27.1 1.0
C5 C:1N1501 3.9 31.4 0.5
C9 C:1N1501 4.0 30.3 0.5
C7 C:1N1501 4.0 30.4 0.5
C7 C:1N1501 4.0 31.5 0.5
C C:GLY329 4.1 31.1 1.0
C2 C:1N1501 4.2 36.1 1.0
O C:HOH630 4.2 50.5 1.0
CA C:ASP330 4.4 31.9 1.0
CG C:ASP330 4.4 33.4 1.0
C8 C:1N1501 4.5 30.1 0.5
C6 C:1N1501 4.5 31.4 0.5
NZ C:LYS219 4.6 27.1 1.0
CB C:ASP330 4.7 32.1 1.0
O C:HOH643 4.7 44.1 1.0
CE C:LYS219 4.7 26.8 1.0
CG C:LEU248 4.7 32.9 1.0
CG C:LEU319 4.7 28.9 1.0
C1 C:1N1501 4.8 36.5 1.0
CB C:LEU248 4.9 31.8 1.0
CG2 C:THR264 4.9 27.3 1.0
OG1 C:THR264 4.9 29.4 1.0

Chlorine binding site 7 out of 8 in 5h2u

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Chlorine binding site 7 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:33.0
occ:0.50
CL D:1N1504 0.0 33.0 0.5
C10 D:1N1504 0.1 32.6 0.5
C9 D:1N1504 1.6 32.6 0.5
C5 D:1N1504 1.7 33.0 0.5
C8 D:1N1504 2.6 32.1 0.5
C4 D:1N1504 2.6 33.4 0.5
C6 D:1N1504 2.7 32.4 0.5
C4 D:1N1504 2.7 33.6 0.5
N2 D:1N1504 2.9 34.4 1.0
O D:ALA217 3.1 32.5 1.0
O D:ILE262 3.2 32.1 1.0
C D:ALA217 3.4 32.7 1.0
N D:LYS219 3.6 32.3 1.0
C3 D:1N1504 3.6 36.5 1.0
N D:THR264 3.6 31.1 1.0
OG1 D:THR264 3.7 29.4 1.0
CB D:ALA217 3.8 32.5 1.0
N D:ILE218 3.8 32.6 1.0
C7 D:1N1504 3.8 32.6 0.5
C5 D:1N1504 3.9 32.9 0.5
CA D:ILE218 3.9 32.5 1.0
C7 D:1N1504 3.9 32.9 0.5
C D:ILE218 4.0 32.3 1.0
C9 D:1N1504 4.0 33.1 0.5
O D:1N1504 4.0 35.7 1.0
CG D:LYS219 4.0 31.3 1.0
CA D:ILE263 4.0 31.6 1.0
C D:ILE262 4.1 32.1 1.0
CG2 D:THR264 4.1 29.8 1.0
C D:ILE263 4.2 31.4 1.0
CA D:ALA217 4.2 32.8 1.0
CB D:LYS219 4.3 31.8 1.0
CB D:THR264 4.3 30.7 1.0
C6 D:1N1504 4.3 32.4 0.5
N D:ILE263 4.4 31.7 1.0
C2 D:1N1504 4.4 36.0 1.0
C8 D:1N1504 4.4 32.7 0.5
CA D:LYS219 4.5 32.0 1.0
CA D:THR264 4.6 30.7 1.0
O D:ILE218 4.8 31.8 1.0
CD D:LYS219 4.8 30.8 1.0
NZ D:LYS219 4.8 32.6 1.0
CG1 D:VAL205 4.9 37.8 1.0
C1 D:1N1504 4.9 36.4 1.0
N D:ALA217 5.0 33.1 1.0

Chlorine binding site 8 out of 8 in 5h2u

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Chlorine binding site 8 out of 8 in the Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of PTK6 Kinase Domain Complexed with Dasatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:32.7
occ:0.50
CL D:1N1504 0.0 32.7 0.5
C10 D:1N1504 0.2 32.9 0.5
C9 D:1N1504 1.6 33.1 0.5
C5 D:1N1504 1.7 32.9 0.5
C4 D:1N1504 2.6 33.6 0.5
C8 D:1N1504 2.6 32.7 0.5
C4 D:1N1504 2.7 33.4 0.5
C6 D:1N1504 2.7 32.4 0.5
N2 D:1N1504 2.9 34.4 1.0
C3 D:1N1504 3.4 36.5 1.0
N D:ASP330 3.4 30.3 1.0
O D:HOH670 3.5 37.2 1.0
O D:1N1504 3.6 35.7 1.0
CA D:GLY329 3.7 29.6 1.0
OD1 D:ASP330 3.8 35.1 1.0
C5 D:1N1504 3.9 33.0 0.5
CD2 D:LEU248 3.9 31.9 1.0
C7 D:1N1504 3.9 32.9 0.5
C D:GLY329 3.9 29.8 1.0
C9 D:1N1504 4.0 32.6 0.5
NZ D:LYS219 4.0 32.6 1.0
C7 D:1N1504 4.0 32.6 0.5
CD2 D:LEU319 4.0 26.1 1.0
O D:HOH624 4.2 42.6 1.0
CA D:ASP330 4.2 30.8 1.0
C2 D:1N1504 4.3 36.0 1.0
C6 D:1N1504 4.4 32.4 0.5
C8 D:1N1504 4.5 32.1 0.5
CB D:ASP330 4.5 31.1 1.0
CG D:ASP330 4.6 33.9 1.0
CG D:LEU248 4.6 31.5 1.0
CB D:LEU248 4.8 30.8 1.0
C1 D:1N1504 4.8 36.4 1.0
CG2 D:THR264 4.8 29.8 1.0
O D:GLY329 5.0 29.3 1.0
CG D:LEU319 5.0 28.2 1.0

Reference:

M.K.Thakur, S.Birudukota, S.Swaminathan, S.K.Battula, S.Vadivelu, R.Tyagi, R.Gosu. Co-Crystal Structures of PTK6: with Dasatinib at 2.24 Angstrom , with Novel Imidazo[1,2-A]Pyrazin-8-Amine Derivative Inhibitor at 1.70 Angstrom Resolution Biochem. Biophys. Res. V. 482 1289 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27993680
DOI: 10.1016/J.BBRC.2016.12.030
Page generated: Fri Jul 26 08:42:04 2024

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