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Chlorine in PDB 5oct: Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.

Protein crystallography data

The structure of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method., PDB code: 5oct was solved by A.Cruz-Migoni, M.T.Ehebauer, S.E.V.Phillips, C.E.Quevedo, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.72 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.490, 118.450, 155.360, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.8

Other elements in 5oct:

The structure of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. (pdb code 5oct). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method., PDB code: 5oct:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5oct

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Chlorine binding site 1 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:65.6
occ:1.00
CL A:9R5202 0.0 65.6 1.0
C2 A:9R5202 1.7 52.5 1.0
C1 A:9R5202 2.7 48.3 1.0
C3 A:9R5202 2.7 55.6 1.0
NE2 A:GLN99 3.1 44.2 1.0
CD A:GLN99 3.7 43.1 1.0
O A:HIS95 3.7 27.7 1.0
CB A:GLN99 3.9 36.4 1.0
CD1 A:TYR96 4.0 23.4 1.0
C6 A:9R5202 4.0 61.9 1.0
C4 A:9R5202 4.0 54.7 1.0
CG A:HIS61 4.0 78.0 1.0
CB A:HIS61 4.0 69.4 1.0
C A:HIS95 4.0 26.4 1.0
O A:HOH346 4.0 41.1 1.0
CE1 A:TYR96 4.1 23.9 1.0
OE1 A:GLN99 4.1 46.3 1.0
CD2 A:HIS61 4.1 77.8 1.0
N A:TYR96 4.2 28.2 1.0
CG A:GLN99 4.3 41.8 1.0
CA A:TYR96 4.3 24.2 1.0
CB A:HIS95 4.4 28.7 1.0
C5 A:9R5202 4.5 62.5 1.0
CG A:TYR96 4.5 24.8 1.0
ND1 A:HIS61 4.5 82.3 1.0
CZ A:TYR96 4.7 27.5 1.0
O A:HOH379 4.8 58.5 1.0
NE2 A:HIS61 4.8 79.9 1.0
CA A:HIS95 4.8 25.6 1.0
CE1 A:HIS61 5.0 90.1 1.0

Chlorine binding site 2 out of 9 in 5oct

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Chlorine binding site 2 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:56.7
occ:1.00
CL B:9R5202 0.0 56.7 1.0
C2 B:9R5202 1.7 49.9 1.0
C1 B:9R5202 2.7 53.4 1.0
C3 B:9R5202 2.7 51.4 1.0
OG1 B:THR74 3.2 69.9 1.0
N B:GLY75 3.7 35.1 1.0
CA B:GLY75 3.7 32.7 1.0
CG2 B:VAL7 3.7 30.9 1.0
CD B:LYS5 3.7 58.5 1.0
CB B:LYS5 3.9 39.4 1.0
C6 B:9R5202 4.0 56.5 1.0
C4 B:9R5202 4.0 53.8 1.0
C B:THR74 4.0 46.8 1.0
O B:TYR71 4.0 67.3 1.0
CB B:THR74 4.3 52.6 1.0
O B:THR74 4.3 47.9 1.0
CB B:LEU56 4.3 26.0 1.0
CG B:LYS5 4.4 46.8 1.0
C5 B:9R5202 4.5 62.3 1.0
CD2 B:LEU56 4.6 32.3 1.0
O B:LEU6 4.6 27.0 1.0
CA B:THR74 4.7 48.0 1.0
C B:LYS5 4.7 29.4 1.0
CA B:LYS5 4.7 33.2 1.0
CE B:LYS5 4.7 64.0 1.0
C B:TYR71 4.9 69.9 1.0
CA B:TYR71 4.9 75.9 1.0
N B:LEU6 5.0 27.8 1.0

Chlorine binding site 3 out of 9 in 5oct

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Chlorine binding site 3 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:73.2
occ:1.00
CL C:9R5202 0.0 73.2 1.0
C2 C:9R5202 1.7 76.9 1.0
C3 C:9R5202 2.7 79.0 1.0
C1 C:9R5202 2.7 78.5 1.0
OG1 C:THR74 3.1 69.3 1.0
CG2 C:VAL7 3.7 35.0 1.0
N C:GLY75 3.8 37.5 1.0
O C:TYR71 3.8 59.8 1.0
CA C:GLY75 3.9 31.4 1.0
C6 C:9R5202 4.0 93.8 1.0
C4 C:9R5202 4.0 89.3 1.0
C C:THR74 4.1 44.2 1.0
CB C:THR74 4.2 57.1 1.0
CD2 C:LEU56 4.2 43.5 1.0
CB C:LEU56 4.3 37.5 1.0
CA C:TYR71 4.5 63.4 1.0
CD C:LYS5 4.5 53.3 1.0
O C:THR74 4.5 47.5 1.0
C5 C:9R5202 4.5 97.9 1.0
CB C:LYS5 4.5 40.1 1.0
C C:TYR71 4.5 57.1 1.0
CB C:TYR71 4.5 55.9 1.0
CA C:THR74 4.7 51.7 1.0
CG C:LEU56 4.9 39.5 1.0
O C:LEU6 5.0 32.6 1.0

Chlorine binding site 4 out of 9 in 5oct

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Chlorine binding site 4 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:67.7
occ:1.00
CL D:9R5202 0.0 67.7 1.0
C2 D:9R5202 1.7 75.0 1.0
C3 D:9R5202 2.7 74.3 1.0
C1 D:9R5202 2.7 68.7 1.0
OG1 D:THR74 3.2 59.3 1.0
N D:GLY75 3.6 34.4 1.0
CG2 D:VAL7 3.6 30.1 1.0
CA D:GLY75 3.6 34.2 1.0
O D:TYR71 3.9 62.9 1.0
C D:THR74 3.9 40.5 1.0
C6 D:9R5202 4.0 80.0 1.0
C4 D:9R5202 4.0 79.0 1.0
CB D:LYS5 4.2 41.0 1.0
CB D:THR74 4.2 52.5 1.0
O D:THR74 4.2 38.6 1.0
CB D:LEU56 4.3 35.1 1.0
CD D:LYS5 4.4 54.6 1.0
C5 D:9R5202 4.5 83.3 1.0
CD2 D:LEU56 4.5 41.6 1.0
CA D:THR74 4.6 47.0 1.0
O D:HOH347 4.6 55.1 1.0
C D:TYR71 4.7 62.4 1.0
O D:LEU6 4.7 28.8 1.0
CA D:TYR71 4.7 66.3 1.0
CG D:LYS5 4.8 47.2 1.0
C D:LYS5 4.9 30.2 1.0
CB D:TYR71 4.9 67.6 1.0
CG D:LEU56 5.0 40.0 1.0
CA D:LYS5 5.0 32.1 1.0

Chlorine binding site 5 out of 9 in 5oct

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Chlorine binding site 5 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:0.5
occ:1.00
CL D:9R5203 0.0 0.5 1.0
C2 D:9R5203 1.7 0.3 1.0
C3 D:9R5203 2.7 0.2 1.0
C1 D:9R5203 2.7 0.6 1.0
OE1 D:GLN99 3.3 92.8 1.0
NH2 D:ARG68 3.3 89.2 1.0
NE2 D:GLN99 3.4 86.1 1.0
CD D:GLN99 3.4 84.1 1.0
CD1 D:TYR96 4.0 34.3 1.0
C6 D:9R5203 4.0 0.6 1.0
C4 D:9R5203 4.0 1.0 1.0
O D:HIS95 4.0 43.3 1.0
CZ D:ARG68 4.0 90.8 1.0
CE1 D:TYR96 4.1 34.7 1.0
C D:HIS95 4.1 43.8 1.0
N D:TYR96 4.2 41.6 1.0
CB D:GLN99 4.2 55.8 1.0
CA D:TYR96 4.3 38.0 1.0
CG D:TYR96 4.4 36.3 1.0
CB D:HIS95 4.4 50.6 1.0
CG D:GLN99 4.5 66.9 1.0
C5 D:9R5203 4.5 0.0 1.0
CZ D:TYR96 4.5 34.3 1.0
NH1 D:ARG68 4.6 86.6 1.0
NE D:ARG68 4.7 95.1 1.0
CD2 D:TYR96 4.9 35.8 1.0
O D:HOH319 4.9 59.8 1.0
CE2 D:TYR96 4.9 36.2 1.0
CA D:HIS95 5.0 46.9 1.0
CB D:TYR96 5.0 34.6 1.0

Chlorine binding site 6 out of 9 in 5oct

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Chlorine binding site 6 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:0.9
occ:1.00
CL E:9R5202 0.0 0.9 1.0
C2 E:9R5202 1.7 94.6 1.0
C3 E:9R5202 2.7 95.1 1.0
C1 E:9R5202 2.7 91.9 1.0
OG1 E:THR74 3.0 61.0 1.0
N E:GLY75 3.4 39.5 1.0
CA E:GLY75 3.5 35.9 1.0
CG2 E:VAL7 3.6 33.1 1.0
O E:TYR71 3.6 73.0 1.0
C E:THR74 3.8 47.4 1.0
C6 E:9R5202 4.0 0.4 1.0
C4 E:9R5202 4.0 96.2 1.0
CB E:THR74 4.1 54.1 1.0
O E:THR74 4.2 50.4 1.0
CB E:LYS5 4.3 37.2 1.0
CD E:LYS5 4.4 60.5 1.0
CA E:THR74 4.4 51.0 1.0
C E:TYR71 4.4 71.2 1.0
C5 E:9R5202 4.5 0.4 1.0
CA E:TYR71 4.5 81.0 1.0
CD2 E:LEU56 4.5 49.5 1.0
CB E:LEU56 4.5 36.7 1.0
CB E:TYR71 4.7 91.7 1.0
O E:LEU6 4.9 34.4 1.0
CG E:LYS5 4.9 46.1 1.0
C E:GLY75 4.9 36.8 1.0
N E:THR74 5.0 46.8 1.0
C E:LYS5 5.0 30.8 1.0

Chlorine binding site 7 out of 9 in 5oct

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Chlorine binding site 7 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl203

b:0.8
occ:1.00
CL E:9R5203 0.0 0.8 1.0
C2 E:9R5203 1.7 0.5 1.0
C3 E:9R5203 2.7 0.7 1.0
C1 E:9R5203 2.7 0.1 1.0
NE2 E:GLN99 3.1 98.7 1.0
OE1 E:GLN99 3.3 0.8 1.0
CD E:GLN99 3.3 0.1 1.0
NH2 E:ARG68 3.4 0.6 1.0
C6 E:9R5203 4.0 0.2 1.0
C4 E:9R5203 4.0 0.8 1.0
CD1 E:TYR96 4.0 42.9 1.0
CZ E:ARG68 4.0 0.5 1.0
O E:HIS95 4.0 42.8 1.0
CE1 E:TYR96 4.1 40.8 1.0
C E:HIS95 4.2 51.4 1.0
CB E:GLN99 4.2 67.5 1.0
N E:TYR96 4.3 48.4 1.0
CA E:TYR96 4.3 46.7 1.0
CG E:GLN99 4.4 87.2 1.0
NH1 E:ARG68 4.4 1.0 1.0
CG E:TYR96 4.4 44.5 1.0
CB E:HIS95 4.5 61.3 1.0
C5 E:9R5203 4.5 0.5 1.0
CZ E:TYR96 4.6 45.4 1.0
NE E:ARG68 4.7 0.3 1.0
CD2 E:TYR96 4.9 48.4 1.0
CE2 E:TYR96 5.0 48.8 1.0
CA E:HIS95 5.0 51.0 1.0

Chlorine binding site 8 out of 9 in 5oct

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Chlorine binding site 8 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl202

b:63.6
occ:1.00
CL F:9R5202 0.0 63.6 1.0
C2 F:9R5202 1.7 67.3 1.0
C1 F:9R5202 2.7 58.2 1.0
C3 F:9R5202 2.7 64.8 1.0
CA F:GLY75 3.3 39.3 1.0
CG2 F:VAL7 3.3 33.2 1.0
N F:GLY75 3.4 46.6 1.0
OG1 F:THR74 3.4 80.5 1.0
O F:TYR71 3.7 82.3 1.0
C F:THR74 3.8 54.0 1.0
CB F:LYS5 3.9 42.5 1.0
C4 F:9R5202 4.0 69.3 1.0
C6 F:9R5202 4.0 68.1 1.0
CD F:LYS5 4.1 62.5 1.0
O F:THR74 4.2 44.0 1.0
CB F:THR74 4.4 68.0 1.0
CB F:LEU56 4.4 38.9 1.0
C5 F:9R5202 4.5 73.4 1.0
O F:LEU6 4.5 33.1 1.0
C F:LYS5 4.6 37.7 1.0
CG F:LYS5 4.6 48.1 1.0
C F:TYR71 4.6 84.6 1.0
CA F:THR74 4.6 58.1 1.0
CD2 F:LEU56 4.6 48.4 1.0
C F:GLY75 4.7 37.2 1.0
CA F:LYS5 4.7 35.7 1.0
O F:LYS5 4.8 30.4 1.0
CA F:TYR71 4.8 92.1 1.0
CB F:VAL7 4.8 31.6 1.0
C F:LEU6 4.8 30.5 1.0
N F:LEU6 4.8 33.0 1.0
CB F:TYR71 5.0 98.8 1.0

Chlorine binding site 9 out of 9 in 5oct

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Chlorine binding site 9 out of 9 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl203

b:82.5
occ:1.00
CL F:9R5203 0.0 82.5 1.0
C2 F:9R5203 1.7 76.0 1.0
C1 F:9R5203 2.7 82.9 1.0
C3 F:9R5203 2.7 75.5 1.0
OE1 F:GLN99 3.0 0.7 1.0
CD F:GLN99 3.2 90.2 1.0
NE2 F:GLN99 3.2 88.6 1.0
NH1 F:ARG68 3.3 0.7 1.0
CZ F:ARG68 3.6 0.3 1.0
CD1 F:TYR96 3.6 36.1 1.0
CE1 F:TYR96 3.7 36.7 1.0
C4 F:9R5203 4.0 93.9 1.0
NH2 F:ARG68 4.0 0.5 1.0
C6 F:9R5203 4.0 93.3 1.0
CB F:GLN99 4.1 53.8 1.0
O F:HIS95 4.1 38.1 1.0
CG F:GLN99 4.2 70.7 1.0
NE F:ARG68 4.2 0.2 1.0
CA F:TYR96 4.3 37.0 1.0
CG F:TYR96 4.3 37.6 1.0
C F:HIS95 4.4 40.4 1.0
N F:TYR96 4.4 37.9 1.0
CZ F:TYR96 4.4 35.6 1.0
C5 F:9R5203 4.5 98.5 1.0
CB F:HIS95 4.8 39.0 1.0
CD2 F:TYR96 4.9 39.1 1.0
CE2 F:TYR96 4.9 37.2 1.0
CB F:TYR96 4.9 37.0 1.0

Reference:

C.E.Quevedo, A.Cruz-Migoni, N.Bery, A.Miller, T.Tanaka, D.Petch, C.J.R.Bataille, L.Y.W.Lee, P.S.Fallon, H.Tulmin, M.T.Ehebauer, N.Fernandez-Fuentes, A.J.Russell, S.B.Carr, S.E.V.Phillips, T.H.Rabbitts. Small Molecule Inhibitors of Ras-Effector Protein Interactions Derived Using An Intracellular Antibody Fragment. Nat Commun V. 9 3169 2018.
ISSN: ESSN 2041-1723
PubMed: 30093669
DOI: 10.1038/S41467-018-05707-2
Page generated: Fri Jul 26 14:24:19 2024

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