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Fluorine in PDB 4op1: Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate

Protein crystallography data

The structure of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate, PDB code: 4op1 was solved by S.R.Jordan, S.Chmait, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.39
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 149.180, 149.180, 132.105, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 26.8

Other elements in 4op1:

The structure of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Iodine (I) 28 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate (pdb code 4op1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate, PDB code: 4op1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 1 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:72.3
occ:1.00
F2 A:2UW701 0.0 72.3 1.0
C17 A:2UW701 1.3 57.7 1.0
F3 A:2UW701 2.2 63.5 1.0
F1 A:2UW701 2.2 63.0 1.0
C10 A:2UW701 2.2 48.0 1.0
C11 A:2UW701 2.5 41.6 1.0
C6 A:2UW701 2.8 41.8 1.0
C7 A:2UW701 2.9 42.3 1.0
CE1 A:HIS504 3.0 41.5 1.0
ND1 A:HIS504 3.2 38.2 1.0
O1 A:2UW701 3.4 44.5 1.0
NE2 A:HIS504 3.8 43.0 1.0
CG A:MET522 3.9 34.3 1.0
N1 A:2UW701 4.1 39.8 1.0
CG A:HIS504 4.2 41.3 1.0
C8 A:2UW701 4.2 39.9 1.0
O A:HOH817 4.4 27.6 1.0
CD2 A:HIS504 4.5 40.4 1.0
O A:GLU32 4.6 32.2 1.0
O A:HOH801 4.9 41.1 1.0
CA A:MET522 4.9 35.0 1.0
SD A:MET522 4.9 37.7 1.0
CB A:SER255 4.9 35.5 1.0

Fluorine binding site 2 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 2 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:63.5
occ:1.00
F3 A:2UW701 0.0 63.5 1.0
C17 A:2UW701 1.3 57.7 1.0
F1 A:2UW701 2.2 63.0 1.0
F2 A:2UW701 2.2 72.3 1.0
C10 A:2UW701 2.3 48.0 1.0
O1 A:2UW701 2.8 44.5 1.0
C7 A:2UW701 2.8 42.3 1.0
O A:HOH801 3.0 41.1 1.0
O A:ALA521 3.1 34.8 1.0
C A:ALA521 3.2 34.4 1.0
C6 A:2UW701 3.3 41.8 1.0
N A:MET522 3.4 36.0 1.0
CA A:MET522 3.5 35.0 1.0
C11 A:2UW701 3.6 41.6 1.0
CB A:ARG525 3.6 50.8 1.0
CB A:ALA521 3.7 29.8 1.0
CG A:MET522 3.7 34.3 1.0
C8 A:2UW701 3.8 39.9 1.0
CA A:ALA521 4.1 31.7 1.0
CB A:MET522 4.2 33.9 1.0
CG A:ARG525 4.2 55.7 1.0
N1 A:2UW701 4.3 39.8 1.0
C A:MET522 4.6 39.9 1.0
NE A:ARG525 4.7 70.5 1.0
CE1 A:HIS504 4.8 41.5 1.0
C9 A:2UW701 4.8 43.6 1.0
O A:MET522 4.9 42.1 1.0
CA A:ARG525 4.9 47.0 1.0
O A:ARG518 5.0 37.0 1.0
N A:ARG525 5.0 45.3 1.0

Fluorine binding site 3 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 3 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:63.0
occ:1.00
F1 A:2UW701 0.0 63.0 1.0
C17 A:2UW701 1.3 57.7 1.0
F3 A:2UW701 2.2 63.5 1.0
F2 A:2UW701 2.2 72.3 1.0
C10 A:2UW701 2.2 48.0 1.0
O1 A:2UW701 2.5 44.5 1.0
C11 A:2UW701 2.7 41.6 1.0
NE A:ARG525 3.2 70.5 1.0
CG A:ARG525 3.3 55.7 1.0
CB A:ARG525 3.5 50.8 1.0
CE1 A:HIS504 3.6 41.5 1.0
C7 A:2UW701 3.6 42.3 1.0
CD A:ARG525 3.8 57.2 1.0
NE2 A:HIS504 3.8 43.0 1.0
O A:HOH801 3.9 41.1 1.0
CZ A:ARG525 4.1 76.1 1.0
NH2 A:ARG525 4.2 71.6 1.0
C6 A:2UW701 4.3 41.8 1.0
ND1 A:HIS504 4.4 38.2 1.0
C8 A:2UW701 4.6 39.9 1.0
O A:ALA521 4.7 34.8 1.0
CD2 A:HIS504 4.8 40.4 1.0
CA A:ARG525 5.0 47.0 1.0

Fluorine binding site 4 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 4 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:45.2
occ:1.00
F2 B:2UW701 0.0 45.2 1.0
C17 B:2UW701 1.5 50.2 1.0
C11 B:2UW701 2.0 42.3 1.0
C10 B:2UW701 2.1 39.6 1.0
F1 B:2UW701 2.4 58.1 1.0
F3 B:2UW701 2.5 44.4 1.0
C7 B:2UW701 2.8 36.6 1.0
C6 B:2UW701 3.0 35.8 1.0
CE1 B:HIS504 3.0 31.2 1.0
O1 B:2UW701 3.3 35.9 1.0
O B:GLU32 3.4 33.1 1.0
ND1 B:HIS504 3.7 31.1 1.0
O B:HOH891 3.9 35.5 1.0
NE2 B:HIS504 4.0 33.4 1.0
C8 B:2UW701 4.0 40.0 1.0
N B:SER34 4.1 31.5 1.0
N1 B:2UW701 4.3 38.8 1.0
O B:HOH839 4.3 36.5 1.0
C B:LYS33 4.4 32.5 1.0
CB B:SER255 4.5 32.4 1.0
CB B:SER34 4.5 32.2 1.0
C B:GLU32 4.5 31.9 1.0
CA B:SER34 4.6 33.0 1.0
OG B:SER255 4.6 37.0 1.0
CA B:LYS33 4.7 34.4 1.0
O B:HOH803 4.8 42.1 1.0
O B:LYS33 4.9 35.2 1.0
CG B:HIS504 4.9 31.8 1.0
I B:IOD711 5.0 66.5 0.6

Fluorine binding site 5 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 5 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:44.4
occ:1.00
F3 B:2UW701 0.0 44.4 1.0
C17 B:2UW701 1.3 50.2 1.0
F1 B:2UW701 2.0 58.1 1.0
C10 B:2UW701 2.2 39.6 1.0
F2 B:2UW701 2.5 45.2 1.0
C7 B:2UW701 2.7 36.6 1.0
C6 B:2UW701 2.7 35.8 1.0
O1 B:2UW701 2.8 35.9 1.0
C11 B:2UW701 3.4 42.3 1.0
CG B:MET522 3.8 33.4 1.0
CE1 B:HIS504 3.9 31.2 1.0
C8 B:2UW701 3.9 40.0 1.0
O B:HOH801 3.9 36.3 1.0
N1 B:2UW701 4.0 38.8 1.0
CA B:MET522 4.1 32.0 1.0
O B:ALA521 4.1 30.9 1.0
C B:ALA521 4.1 31.2 1.0
N B:MET522 4.1 30.3 1.0
ND1 B:HIS504 4.2 31.1 1.0
CB B:ALA521 4.3 29.6 1.0
CB B:ARG525 4.3 44.2 1.0
O B:HOH839 4.4 36.5 1.0
NE2 B:HIS504 4.4 33.4 1.0
CB B:MET522 4.5 31.9 1.0
CG B:ARG525 4.7 48.7 1.0
C9 B:2UW701 4.9 45.6 1.0
O B:HOH891 4.9 35.5 1.0
CG B:HIS504 4.9 31.8 1.0
CA B:ALA521 4.9 30.8 1.0
C5 B:2UW701 4.9 41.2 1.0
NE B:ARG525 4.9 65.0 1.0

Fluorine binding site 6 out of 6 in 4op1

Go back to Fluorine Binding Sites List in 4op1
Fluorine binding site 6 out of 6 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:58.1
occ:1.00
F1 B:2UW701 0.0 58.1 1.0
C17 B:2UW701 1.3 50.2 1.0
F3 B:2UW701 2.0 44.4 1.0
C10 B:2UW701 2.3 39.6 1.0
F2 B:2UW701 2.4 45.2 1.0
O1 B:2UW701 2.4 35.9 1.0
C11 B:2UW701 2.8 42.3 1.0
NE B:ARG525 3.2 65.0 1.0
CE1 B:HIS504 3.5 31.2 1.0
CG B:ARG525 3.5 48.7 1.0
O B:HOH803 3.5 42.1 1.0
C7 B:2UW701 3.6 36.6 1.0
CB B:ARG525 3.6 44.2 1.0
NE2 B:HIS504 3.6 33.4 1.0
CD B:ARG525 3.9 53.4 1.0
CZ B:ARG525 4.0 80.1 1.0
NH2 B:ARG525 4.1 75.9 1.0
O B:HOH801 4.1 36.3 1.0
C6 B:2UW701 4.2 35.8 1.0
ND1 B:HIS504 4.4 31.1 1.0
CD2 B:HIS504 4.6 33.8 1.0
C8 B:2UW701 4.7 40.0 1.0
CG B:HIS504 5.0 31.8 1.0

Reference:

N.Tamayo, M.H.Norman, M.D.Bartberger, Y.Bo, J.Chen, R.Cupples, C.Fotsch, C.Hale, F-T Hong, S.R.Jordan, L.Liu, D.J.Lloyd, C.Moyer, N.Nishimura, G.Sivits, S.Tadesse, G.Van, K.C.Yang, D.J.St. Jean. Small Molecule Disruptors of the Glucokinase- Glucokinase Regulatory Protein Interaction:5. New Aryl Sulfones Series, Optimization Through Conformational Analysis J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
Page generated: Sun Dec 13 12:09:53 2020

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