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Chlorine in PDB 5k0k: Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434

Enzymatic activity of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434

All present enzymatic activity of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434, PDB code: 5k0k was solved by X.Wang, J.Liu, W.Zhang, M.A.Stashko, J.Nichols, D.Deryckere, M.J.Miley, J.Norris-Drouin, Z.Chen, M.Machius, E.Wood, D.K.Graham, H.S.Earp, K.Graham, D.Kireev, S.V.Frye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.072, 91.315, 69.203, 90.00, 100.42, 90.00
R / Rfree (%) 19.8 / 25.4

Other elements in 5k0k:

The structure of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 (pdb code 5k0k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434, PDB code: 5k0k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:46.9
occ:1.00
 HH12 A:ARG732 2.0 58.8 1.0
HB2 A:ARG651 2.5 70.6 1.0
HH22 A:ARG732 2.5 55.5 1.0
H A:ARG651 2.6 50.0 1.0
HE A:ARG651 2.7 95.3 1.0
HB3 A:ARG651 2.8 70.6 1.0
NH1 A:ARG732 2.8 49.0 1.0
HG2 A:PRO672 2.9 44.5 1.0
CB A:ARG651 3.0 58.9 1.0
NH2 A:ARG732 3.2 46.3 1.0
N A:ARG651 3.2 41.7 1.0
HH21 A:ARG651 3.3 99.5 1.0
HH11 A:ARG732 3.4 58.8 1.0
CZ A:ARG732 3.4 47.1 1.0
HA A:ILE650 3.5 41.4 1.0
NE A:ARG651 3.5 79.4 1.0
HG13 A:ILE650 3.8 41.1 1.0
CA A:ARG651 3.8 49.7 1.0
CG A:PRO672 3.8 37.0 1.0
NH2 A:ARG651 3.9 83.0 1.0
HH21 A:ARG732 4.0 55.5 1.0
HG3 A:PRO672 4.1 44.5 1.0
C A:ILE650 4.1 37.7 1.0
CZ A:ARG651 4.2 83.8 1.0
CA A:ILE650 4.2 34.5 1.0
CG A:ARG651 4.3 66.0 1.0
O A:VAL649 4.3 39.6 1.0
HA A:ARG651 4.3 59.7 1.0
HB2 A:PRO672 4.4 40.7 1.0
CD A:ARG651 4.4 74.2 1.0
CB A:PRO672 4.5 33.9 1.0
CG1 A:ILE650 4.5 34.2 1.0
HG3 A:ARG651 4.6 79.3 1.0
HG12 A:ILE650 4.6 41.1 1.0
HD2 A:PRO672 4.6 41.2 1.0
HH22 A:ARG651 4.7 99.5 1.0
HB3 A:PRO672 4.7 40.7 1.0
NE A:ARG732 4.7 42.9 1.0
CD A:PRO672 4.7 34.3 1.0
HD2 A:ARG651 4.9 89.0 1.0
C A:ARG651 4.9 50.6 1.0
O A:ARG651 5.0 56.9 1.0

Chlorine binding site 2 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:40.8
occ:1.00
 HD2 A:PRO802 2.6 39.3 1.0
H A:LYS820 2.6 42.7 1.0
HA A:TYR801 3.0 48.7 1.0
HD23 A:LEU819 3.1 31.3 1.0
HA A:LEU819 3.2 37.3 1.0
HG3 A:LYS820 3.2 54.6 1.0
HD13 B:LEU688 3.3 60.3 1.0
H A:TYR801 3.4 49.5 1.0
N A:LYS820 3.5 35.6 1.0
HB2 A:LYS820 3.5 50.0 1.0
CD A:PRO802 3.6 32.8 1.0
HD11 B:LEU688 3.7 60.3 1.0
HD2 A:LYS820 3.7 59.6 1.0
HZ2 A:TRP791 3.7 36.8 1.0
CA A:TYR801 3.8 40.6 1.0
HG2 A:PRO802 3.9 41.6 1.0
HD22 A:LEU819 3.9 31.3 1.0
CD2 A:LEU819 3.9 26.1 1.0
CG A:LYS820 3.9 45.5 1.0
CD1 B:LEU688 3.9 50.2 1.0
N A:TYR801 3.9 41.2 1.0
CA A:LEU819 4.0 31.1 1.0
CB A:LYS820 4.1 41.7 1.0
HD3 A:PRO802 4.1 39.3 1.0
HD1 A:TYR801 4.1 53.0 1.0
HE3 A:LYS820 4.2 64.4 1.0
CG A:PRO802 4.2 34.7 1.0
CZ2 A:TRP791 4.2 30.6 1.0
CD A:LYS820 4.3 49.7 1.0
C A:LEU819 4.3 33.3 1.0
N A:PRO802 4.4 36.8 1.0
CA A:LYS820 4.4 38.7 1.0
HD12 B:LEU688 4.4 60.3 1.0
HB3 A:LEU819 4.5 33.7 1.0
HD21 A:LEU819 4.5 31.3 1.0
HG3 A:PRO802 4.5 41.6 1.0
CD1 A:TYR801 4.6 44.1 1.0
C A:TYR801 4.6 39.8 1.0
HE1 A:TRP791 4.6 36.9 1.0
HD22 B:LEU688 4.6 57.5 1.0
CB A:LEU819 4.7 28.1 1.0
O A:ARG818 4.7 35.4 1.0
HH A:TYR812 4.7 53.0 1.0
HG2 A:LYS820 4.8 54.6 1.0
CE A:LYS820 4.8 53.7 1.0
CE2 A:TRP791 4.8 28.7 1.0
HD21 B:LEU688 4.9 57.5 1.0
CB A:TYR801 4.9 42.1 1.0
CG A:LEU819 4.9 27.3 1.0
CH2 A:TRP791 4.9 31.9 1.0
HH2 A:TRP791 4.9 38.2 1.0
NE1 A:TRP791 4.9 30.8 1.0
HB3 A:LYS820 5.0 50.0 1.0
O A:LYS820 5.0 39.4 1.0
CG A:TYR801 5.0 42.0 1.0

Chlorine binding site 3 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:64.8
occ:1.00
 HH22 A:ARG584 2.2 67.7 1.0
H A:LEU589 2.4 56.1 1.0
HH12 A:ARG584 2.7 63.2 1.0
HA A:ILE588 2.8 58.2 1.0
NH2 A:ARG584 3.0 56.5 1.0
N A:LEU589 3.2 46.7 1.0
HB2 A:LEU589 3.3 55.4 1.0
NH1 A:ARG584 3.4 52.7 1.0
HH21 A:ARG584 3.6 67.7 1.0
CA A:ILE588 3.6 48.5 1.0
CZ A:ARG584 3.7 53.6 1.0
O A:LEU587 3.7 52.3 1.0
HG23 A:ILE588 3.9 63.9 1.0
HG A:LEU589 3.9 55.0 1.0
C A:ILE588 3.9 46.0 1.0
HD12 A:LEU589 3.9 58.0 1.0
CB A:LEU589 4.0 46.1 1.0
CA A:LEU589 4.2 42.6 1.0
HH11 A:ARG584 4.2 63.2 1.0
HG13 A:ILE588 4.2 67.5 1.0
CG A:LEU589 4.4 45.8 1.0
C A:LEU587 4.5 49.3 1.0
N A:ILE588 4.5 47.7 1.0
CG2 A:ILE588 4.6 53.2 1.0
CB A:ILE588 4.6 51.6 1.0
O A:LEU589 4.6 45.8 1.0
CD1 A:LEU589 4.6 48.3 1.0
HG22 A:ILE588 4.8 63.9 1.0
HB3 A:LEU589 4.8 55.4 1.0
C A:LEU589 4.9 42.5 1.0
CG1 A:ILE588 4.9 56.3 1.0
HA A:LEU589 4.9 51.1 1.0
NE A:ARG584 5.0 51.7 1.0

Chlorine binding site 4 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:48.4
occ:1.00
 HH12 A:ARG687 2.3 63.8 1.0
HH22 B:ARG687 2.8 58.5 0.1
HA A:MET798 2.8 32.5 1.0
HH22 B:ARG687 2.8 58.4 0.9
HA B:MET798 2.9 34.0 1.0
O A:HOH1010 3.0 24.4 1.0
HG2 A:MET798 3.0 41.0 1.0
NH1 A:ARG687 3.1 53.2 1.0
HG2 B:MET798 3.1 36.2 1.0
HH11 A:ARG687 3.3 63.8 1.0
NH2 B:ARG687 3.5 48.7 0.1
NH2 B:ARG687 3.5 48.7 0.9
HG3 B:MET798 3.6 36.2 1.0
HH21 B:ARG687 3.7 58.5 0.1
HH21 B:ARG687 3.7 58.4 0.9
CA A:MET798 3.7 27.1 1.0
CA B:MET798 3.7 28.3 1.0
CG B:MET798 3.8 30.2 1.0
CG A:MET798 3.8 34.2 1.0
HG3 A:MET798 3.8 41.0 1.0
HH22 A:ARG687 4.1 66.3 1.0
O B:GLY797 4.1 29.5 1.0
N A:MET798 4.1 26.2 1.0
N B:MET798 4.1 27.0 1.0
O A:GLY797 4.2 34.8 1.0
CZ A:ARG687 4.2 55.6 1.0
HD22 B:LEU684 4.3 37.7 1.0
H B:THR799 4.3 34.8 1.0
CB A:MET798 4.3 29.6 1.0
CB B:MET798 4.3 29.4 1.0
C B:GLY797 4.3 27.5 1.0
C A:GLY797 4.3 32.4 1.0
HD21 B:LEU684 4.3 37.7 1.0
H A:THR799 4.3 38.4 1.0
HH12 B:ARG687 4.4 63.2 0.1
HD21 A:LEU684 4.4 34.1 1.0
HD22 A:LEU684 4.4 34.1 1.0
HH12 B:ARG687 4.4 63.7 0.9
NH2 A:ARG687 4.5 55.3 1.0
O B:HOH1001 4.5 25.5 1.0
CZ B:ARG687 4.6 50.4 0.1
H A:MET798 4.6 31.5 1.0
H B:MET798 4.6 32.4 1.0
CZ B:ARG687 4.6 50.9 0.9
CD2 B:LEU684 4.6 31.4 1.0
HB3 A:MET798 4.7 35.6 1.0
HB3 B:MET798 4.7 35.2 1.0
CD2 A:LEU684 4.7 28.4 1.0
HD23 B:LEU684 4.7 37.7 1.0
HD23 A:LEU684 4.8 34.1 1.0
NH1 B:ARG687 4.8 52.7 0.1
C A:MET798 4.8 31.7 1.0
NH1 B:ARG687 4.8 53.1 0.9
C B:MET798 4.9 29.2 1.0
N B:THR799 4.9 29.0 1.0
N A:THR799 4.9 32.0 1.0

Chlorine binding site 5 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl901

b:44.7
occ:1.00
 HH22 B:ARG584 2.3 56.0 1.0
H B:LEU589 2.4 49.2 1.0
HA B:ILE588 2.5 52.4 1.0
HH12 B:ARG584 2.7 57.6 1.0
NH2 B:ARG584 3.1 46.6 1.0
N B:LEU589 3.2 41.0 1.0
CA B:ILE588 3.4 43.6 1.0
NH1 B:ARG584 3.4 48.0 1.0
HG B:LEU589 3.6 44.6 1.0
HG22 B:ILE588 3.6 54.7 1.0
CZ B:ARG584 3.7 48.0 1.0
O B:LEU587 3.7 62.4 1.0
HB B:ILE588 3.7 54.1 1.0
HB2 B:LEU589 3.8 44.0 1.0
HH21 B:ARG584 3.8 56.0 1.0
C B:ILE588 3.8 39.8 1.0
CB B:ILE588 4.0 45.1 1.0
HH11 B:ARG584 4.1 57.6 1.0
CB B:LEU589 4.3 36.6 1.0
CG2 B:ILE588 4.3 45.6 1.0
CA B:LEU589 4.3 37.9 1.0
HD12 B:LEU589 4.3 49.2 1.0
CG B:LEU589 4.3 37.2 1.0
N B:ILE588 4.4 48.1 1.0
C B:LEU587 4.4 56.4 1.0
O B:LEU589 4.6 40.5 1.0
HG23 B:ILE588 4.8 54.7 1.0
CD1 B:LEU589 4.8 41.0 1.0
C B:LEU589 5.0 42.6 1.0
HG21 B:ILE588 5.0 54.7 1.0

Chlorine binding site 6 out of 6 in 5k0k

Go back to Chlorine Binding Sites List in 5k0k
Chlorine binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434


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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl902

b:37.1
occ:1.00
 H B:LYS820 2.2 52.1 1.0
HA B:LEU819 2.8 58.2 1.0
HD2 B:PRO802 2.9 37.0 1.0
HG3 B:LYS820 2.9 59.5 1.0
N B:LYS820 3.1 43.4 1.0
HD23 B:LEU819 3.2 63.1 1.0
HA B:TYR801 3.2 48.6 1.0
HD13 A:LEU688 3.3 56.1 1.0
HB2 B:LYS820 3.4 55.1 1.0
H B:TYR801 3.6 47.6 1.0
HD22 B:LEU819 3.7 63.1 1.0
CA B:LEU819 3.7 48.5 1.0
CG B:LYS820 3.7 49.5 1.0
HD2 B:LYS820 3.7 64.2 1.0
HD11 A:LEU688 3.8 56.1 1.0
HZ2 B:TRP791 3.8 49.8 1.0
CD B:PRO802 3.8 30.8 1.0
CD2 B:LEU819 3.9 52.6 1.0
CB B:LYS820 3.9 45.9 1.0
C B:LEU819 3.9 47.7 1.0
CD1 A:LEU688 4.0 46.7 1.0
CA B:LYS820 4.1 42.7 1.0
CA B:TYR801 4.1 40.5 1.0
HG2 B:PRO802 4.1 38.3 1.0
HB3 B:LEU819 4.1 58.5 1.0
HE3 B:LYS820 4.2 69.2 1.0
CD B:LYS820 4.2 53.5 1.0
N B:TYR801 4.2 39.7 1.0
HD1 B:TYR801 4.3 52.7 1.0
CZ2 B:TRP791 4.3 41.5 1.0
HD3 B:PRO802 4.3 37.0 1.0
CB B:LEU819 4.4 48.7 1.0
HD12 A:LEU688 4.4 56.1 1.0
CG B:PRO802 4.5 31.9 1.0
HH B:TYR812 4.5 52.4 1.0
HG2 B:LYS820 4.5 59.5 1.0
O B:ARG818 4.5 43.3 1.0
HD21 B:LEU819 4.6 63.1 1.0
N B:PRO802 4.7 35.0 1.0
HE1 B:TRP791 4.7 49.2 1.0
HD22 A:LEU688 4.7 53.6 1.0
CD1 B:TYR801 4.7 43.9 1.0
HG3 B:PRO802 4.7 38.3 1.0
CE B:LYS820 4.7 57.7 1.0
CG B:LEU819 4.7 49.8 1.0
N B:LEU819 4.8 44.8 1.0
HA B:LYS820 4.8 51.3 1.0
O B:LYS820 4.8 33.5 1.0
HB3 B:LYS820 4.8 55.1 1.0
CE2 B:TRP791 4.8 40.4 1.0
C B:TYR801 4.9 39.6 1.0
C B:LYS820 4.9 38.0 1.0
CH2 B:TRP791 4.9 41.8 1.0
HH2 B:TRP791 5.0 50.2 1.0
NE1 B:TRP791 5.0 41.0 1.0
HD21 A:LEU688 5.0 53.6 1.0

Reference:

X.Wang, J.Liu, W.Zhang, M.A.Stashko, J.Nichols, M.J.Miley, J.Norris-Drouin, Z.Chen, M.Machius, D.Deryckere, E.Wood, D.K.Graham, H.S.Earp, D.Kireev, S.V.Frye. Design and Synthesis of Novel Macrocyclic Mer Tyrosine Kinase Inhibitors. Acs Med Chem Lett V. 7 1044 2016.
ISSN: ISSN 1948-5875
PubMed: 27994735
DOI: 10.1021/ACSMEDCHEMLETT.6B00221
Page generated: Fri Jul 26 10:22:04 2024

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