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Fluorine in PDB 5yy1: Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739

Protein crystallography data

The structure of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739, PDB code: 5yy1 was solved by S.Swaminathan, M.K.Thakur, S.Kandan, A.Gautam, M.Kanavalli, P.Simhadri, R.Gosu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.77 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.391, 51.730, 89.242, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.5

Other elements in 5yy1:

The structure of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 (pdb code 5yy1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739, PDB code: 5yy1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5yy1

Go back to Fluorine Binding Sites List in 5yy1
Fluorine binding site 1 out of 4 in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:29.7
occ:1.00
F1 A:94F203 0.0 29.7 1.0
C2 A:94F203 1.4 29.4 1.0
C22 A:94F203 2.3 29.8 1.0
C3 A:94F203 2.3 29.4 1.0
N4 A:94F203 2.7 29.3 1.0
C23 A:94F203 2.7 31.4 1.0
F28 A:94F203 3.0 33.5 1.0
NE2 A:HIS95 3.1 25.3 1.0
C24 A:94F203 3.3 32.0 1.0
C32 A:94F203 3.4 31.5 1.0
CG A:GLN99 3.5 25.4 1.0
CE2 A:TYR64 3.5 27.0 1.0
C20 A:94F203 3.6 29.5 1.0
C18 A:94F203 3.6 29.1 1.0
C25 A:94F203 3.6 32.9 1.0
CB A:GLN99 3.8 26.0 1.0
OH A:TYR64 3.8 26.6 1.0
CD2 A:HIS95 3.9 25.3 1.0
CE1 A:HIS95 3.9 25.5 1.0
C5 A:94F203 4.0 29.6 1.0
C19 A:94F203 4.1 29.1 1.0
CZ A:TYR64 4.1 26.6 1.0
F27 A:94F203 4.1 31.9 1.0
C29 A:94F203 4.3 32.5 1.0
CD A:GLN99 4.3 25.9 1.0
C31 A:94F203 4.4 32.2 1.0
OE1 A:GLN99 4.4 25.2 1.0
CD2 A:TYR64 4.5 27.3 1.0
CE1 A:TYR96 4.6 24.9 1.0
CD1 A:TYR96 4.7 24.4 1.0
C7 A:94F203 4.7 28.9 1.0
C30 A:94F203 4.8 32.4 1.0
F26 A:94F203 4.9 34.8 1.0
ND1 A:HIS95 4.9 24.7 1.0
CG A:HIS95 4.9 24.8 1.0
N6 A:94F203 4.9 29.7 1.0

Fluorine binding site 2 out of 4 in 5yy1

Go back to Fluorine Binding Sites List in 5yy1
Fluorine binding site 2 out of 4 in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:34.8
occ:1.00
F26 A:94F203 0.0 34.8 1.0
C25 A:94F203 1.4 32.9 1.0
F27 A:94F203 2.2 31.9 1.0
F28 A:94F203 2.2 33.5 1.0
C24 A:94F203 2.4 32.0 1.0
C29 A:94F203 2.7 32.5 1.0
CG1 A:ILE100 3.2 26.8 1.0
CE A:MET72 3.4 35.2 1.0
C23 A:94F203 3.6 31.4 1.0
O A:TYR96 3.7 24.7 1.0
CD1 A:ILE100 3.8 26.9 1.0
CG1 A:VAL9 3.9 20.3 1.0
C30 A:94F203 4.1 32.4 1.0
N A:ILE100 4.1 26.7 1.0
C22 A:94F203 4.2 29.8 1.0
CD1 A:TYR96 4.2 24.4 1.0
CB A:VAL9 4.3 19.8 1.0
CB A:GLN99 4.3 26.0 1.0
CG2 A:VAL9 4.4 20.7 1.0
CB A:ILE100 4.4 27.2 1.0
CA A:ILE100 4.5 27.6 1.0
C A:TYR96 4.5 24.9 1.0
CA A:TYR96 4.5 24.4 1.0
C A:GLN99 4.6 26.4 1.0
CB A:TYR96 4.7 24.5 1.0
C32 A:94F203 4.7 31.5 1.0
C20 A:94F203 4.8 29.5 1.0
F1 A:94F203 4.9 29.7 1.0
C2 A:94F203 4.9 29.4 1.0
CD2 A:PHE78 4.9 22.5 1.0
C31 A:94F203 4.9 32.2 1.0
CL A:94F203 4.9 29.2 1.0
CE2 A:PHE78 5.0 23.4 1.0
CG A:TYR96 5.0 24.0 1.0
SD A:MET72 5.0 35.3 1.0

Fluorine binding site 3 out of 4 in 5yy1

Go back to Fluorine Binding Sites List in 5yy1
Fluorine binding site 3 out of 4 in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:31.9
occ:1.00
F27 A:94F203 0.0 31.9 1.0
C25 A:94F203 1.4 32.9 1.0
F28 A:94F203 2.2 33.5 1.0
F26 A:94F203 2.2 34.8 1.0
C24 A:94F203 2.4 32.0 1.0
C22 A:94F203 2.8 29.8 1.0
C23 A:94F203 2.9 31.4 1.0
C20 A:94F203 3.0 29.5 1.0
CL A:94F203 3.3 29.2 1.0
CG1 A:VAL9 3.4 20.3 1.0
CD1 A:TYR96 3.4 24.4 1.0
C2 A:94F203 3.5 29.4 1.0
CE A:MET72 3.5 35.2 1.0
C29 A:94F203 3.5 32.5 1.0
CB A:VAL9 3.7 19.8 1.0
CE1 A:TYR96 3.8 24.9 1.0
C19 A:94F203 3.8 29.1 1.0
F1 A:94F203 4.1 29.7 1.0
O A:HOH358 4.1 21.8 1.0
C32 A:94F203 4.2 31.5 1.0
C3 A:94F203 4.3 29.4 1.0
C18 A:94F203 4.4 29.1 1.0
CG2 A:VAL9 4.5 20.7 1.0
CG A:TYR96 4.6 24.0 1.0
C30 A:94F203 4.7 32.4 1.0
SD A:MET72 4.7 35.3 1.0
CA A:VAL9 4.9 20.2 1.0
C31 A:94F203 5.0 32.2 1.0

Fluorine binding site 4 out of 4 in 5yy1

Go back to Fluorine Binding Sites List in 5yy1
Fluorine binding site 4 out of 4 in the Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:33.5
occ:1.00
F28 A:94F203 0.0 33.5 1.0
C25 A:94F203 1.4 32.9 1.0
F27 A:94F203 2.2 31.9 1.0
F26 A:94F203 2.2 34.8 1.0
C24 A:94F203 2.3 32.0 1.0
CD1 A:TYR96 3.0 24.4 1.0
F1 A:94F203 3.0 29.7 1.0
C23 A:94F203 3.0 31.4 1.0
C22 A:94F203 3.2 29.8 1.0
C2 A:94F203 3.2 29.4 1.0
C29 A:94F203 3.3 32.5 1.0
CB A:GLN99 3.4 26.0 1.0
CA A:TYR96 3.5 24.4 1.0
CE1 A:TYR96 3.7 24.9 1.0
CG A:TYR96 3.8 24.0 1.0
O A:TYR96 3.8 24.7 1.0
CB A:TYR96 3.9 24.5 1.0
C20 A:94F203 4.1 29.5 1.0
CG A:GLN99 4.1 25.4 1.0
C3 A:94F203 4.1 29.4 1.0
C A:TYR96 4.2 24.9 1.0
C32 A:94F203 4.3 31.5 1.0
C30 A:94F203 4.5 32.4 1.0
O A:HIS95 4.5 24.3 1.0
N A:TYR96 4.6 24.4 1.0
CA A:GLN99 4.6 26.1 1.0
N A:ILE100 4.7 26.7 1.0
N4 A:94F203 4.8 29.3 1.0
CD2 A:HIS95 4.8 25.3 1.0
NE2 A:HIS95 4.8 25.3 1.0
CZ A:TYR96 4.9 24.8 1.0
C19 A:94F203 4.9 29.1 1.0
C A:GLN99 4.9 26.4 1.0
CG1 A:ILE100 4.9 26.8 1.0
C31 A:94F203 4.9 32.2 1.0
C A:HIS95 4.9 24.5 1.0
C18 A:94F203 4.9 29.1 1.0
CD2 A:TYR96 4.9 24.5 1.0
CB A:VAL9 4.9 19.8 1.0
CL A:94F203 4.9 29.2 1.0

Reference:

S.Swaminathan, M.K.Thakur, S.Kandan, A.Gautam, M.Kanavalli, P.Simhadri, R.Gosu. Co-Crystal Structure of Kras (G12C) Covalently Bound with Quinazoline Based Inhibitor JBI739 To Be Published.
Page generated: Thu Aug 1 17:23:15 2024

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