Fluorine in PDB 6w0n: Structure of Khk in Complex with Compound 2

Enzymatic activity of Structure of Khk in Complex with Compound 2

All present enzymatic activity of Structure of Khk in Complex with Compound 2:
2.7.1.3;

Protein crystallography data

The structure of Structure of Khk in Complex with Compound 2, PDB code: 6w0n was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.28 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.800, 86.170, 137.130, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Khk in Complex with Compound 2 (pdb code 6w0n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Khk in Complex with Compound 2, PDB code: 6w0n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 1 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:62.5
occ:1.00
F1 A:RYS301 0.0 62.5 1.0
C15 A:RYS301 1.3 60.2 1.0
F3 A:RYS301 2.1 57.9 1.0
F2 A:RYS301 2.1 62.1 1.0
C8 A:RYS301 2.4 58.6 1.0
C9 A:RYS301 2.6 58.1 1.0
O A:HOH459 3.3 54.3 1.0
CB A:PRO246 3.5 41.9 1.0
C7 A:RYS301 3.7 57.0 1.0
CG2 A:VAL250 3.7 47.9 1.0
C10 A:RYS301 4.0 60.0 1.0
CA A:PRO246 4.2 40.8 1.0
CB A:GLU227 4.2 52.6 1.0
C16 A:RYS301 4.3 52.7 1.0
OE2 A:GLU227 4.4 69.3 1.0
CA A:GLU227 4.5 50.8 1.0
CD A:PRO247 4.5 42.4 1.0
CG1 A:VAL250 4.5 47.8 1.0
CG A:PRO246 4.7 45.3 1.0
C6 A:RYS301 4.7 55.0 1.0
CB A:VAL250 4.8 48.0 1.0
N A:GLU227 4.8 51.1 1.0
O A:HOH440 4.8 54.6 1.0
N2 A:RYS301 4.9 57.2 1.0
N3 A:RYS301 4.9 64.7 1.0
C14 A:RYS301 4.9 66.2 1.0

Fluorine binding site 2 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 2 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:62.1
occ:1.00
F2 A:RYS301 0.0 62.1 1.0
C15 A:RYS301 1.3 60.2 1.0
F3 A:RYS301 2.1 57.9 1.0
F1 A:RYS301 2.1 62.5 1.0
C8 A:RYS301 2.4 58.6 1.0
C16 A:RYS301 2.9 52.7 1.0
C7 A:RYS301 2.9 57.0 1.0
N4 A:RYS301 3.4 52.9 1.0
C9 A:RYS301 3.5 58.1 1.0
CB A:PRO246 3.5 41.9 1.0
CA A:PRO246 3.7 40.8 1.0
CA A:GLU227 3.8 50.8 1.0
CB A:ALA244 3.8 41.6 1.0
N A:PRO246 4.1 41.3 1.0
O A:ALA226 4.2 53.3 1.0
N A:GLU227 4.2 51.1 1.0
C6 A:RYS301 4.3 55.0 1.0
CB A:GLU227 4.3 52.6 1.0
O A:HOH403 4.3 37.7 1.0
CD A:PRO246 4.3 42.3 1.0
C A:ALA226 4.4 54.0 1.0
CG A:PRO246 4.4 45.3 1.0
C10 A:RYS301 4.6 60.0 1.0
C A:PHE245 4.8 43.2 1.0
CD A:PRO247 4.9 42.4 1.0
C A:GLU227 4.9 54.5 1.0
N2 A:RYS301 4.9 57.2 1.0

Fluorine binding site 3 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 3 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:57.9
occ:1.00
F3 A:RYS301 0.0 57.9 1.0
C15 A:RYS301 1.3 60.2 1.0
F2 A:RYS301 2.1 62.1 1.0
F1 A:RYS301 2.1 62.5 1.0
C8 A:RYS301 2.4 58.6 1.0
C7 A:RYS301 3.1 57.0 1.0
C16 A:RYS301 3.1 52.7 1.0
CD A:PRO247 3.2 42.4 1.0
C9 A:RYS301 3.3 58.1 1.0
CA A:PRO246 3.5 40.8 1.0
N4 A:RYS301 3.6 52.9 1.0
CB A:CYS289 3.7 46.7 1.0
CB A:PRO246 3.7 41.9 1.0
SG A:CYS289 3.9 50.8 1.0
CG2 A:VAL250 4.1 47.9 1.0
N A:PRO247 4.2 42.4 1.0
CG A:PRO247 4.4 46.6 1.0
C6 A:RYS301 4.4 55.0 1.0
C A:PRO246 4.4 44.3 1.0
N A:PRO246 4.4 41.3 1.0
CG1 A:VAL250 4.5 47.8 1.0
C10 A:RYS301 4.5 60.0 1.0
CA A:GLY286 4.6 43.9 1.0
O A:GLY286 4.7 46.5 1.0
O A:PHE245 4.8 40.2 1.0
CB A:VAL250 4.9 48.0 1.0
C A:PHE245 5.0 43.2 1.0
N2 A:RYS301 5.0 57.2 1.0

Fluorine binding site 4 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 4 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:77.4
occ:1.00
F1 B:RYS301 0.0 77.4 1.0
C15 B:RYS301 1.3 74.3 1.0
F2 B:RYS301 2.1 76.8 1.0
F3 B:RYS301 2.1 75.5 1.0
C8 B:RYS301 2.4 66.9 1.0
C9 B:RYS301 2.7 66.4 1.0
CG2 B:VAL250 3.6 61.3 1.0
C7 B:RYS301 3.7 58.9 1.0
CB B:PRO246 3.9 50.7 1.0
OE1 B:GLU227 3.9 98.9 1.0
C10 B:RYS301 4.1 68.4 1.0
C16 B:RYS301 4.2 58.1 1.0
CB B:GLU227 4.2 51.8 1.0
CA B:PRO246 4.4 49.1 1.0
CD B:PRO247 4.5 51.2 1.0
CA B:GLU227 4.6 49.3 1.0
C6 B:RYS301 4.7 56.6 1.0
N4 B:RYS301 4.8 58.4 1.0
CD B:GLU227 4.9 97.9 1.0
N2 B:RYS301 4.9 61.9 1.0
N3 B:RYS301 4.9 79.2 1.0
N B:GLU227 4.9 48.9 1.0

Fluorine binding site 5 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 5 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:76.8
occ:1.00
F2 B:RYS301 0.0 76.8 1.0
C15 B:RYS301 1.3 74.3 1.0
F1 B:RYS301 2.1 77.4 1.0
F3 B:RYS301 2.1 75.5 1.0
C8 B:RYS301 2.4 66.9 1.0
C16 B:RYS301 2.9 58.1 1.0
C7 B:RYS301 3.0 58.9 1.0
N4 B:RYS301 3.3 58.4 1.0
C9 B:RYS301 3.4 66.4 1.0
CA B:GLU227 3.5 49.3 1.0
CB B:PRO246 3.7 50.7 1.0
CB B:GLU227 3.9 51.8 1.0
CA B:PRO246 3.9 49.1 1.0
CB B:ALA244 3.9 47.4 1.0
N B:GLU227 4.0 48.9 1.0
O B:ALA226 4.2 52.8 1.0
C6 B:RYS301 4.3 56.6 1.0
C B:ALA226 4.3 52.9 1.0
N B:PRO246 4.3 49.0 1.0
CD B:PRO246 4.5 50.6 1.0
CG B:PRO246 4.6 54.1 1.0
C10 B:RYS301 4.6 68.4 1.0
C B:GLU227 4.6 51.0 1.0
OE1 B:GLU227 4.7 98.9 1.0
O B:HOH409 4.8 40.2 1.0
O B:GLU227 4.8 48.7 1.0
CD B:PRO247 4.9 51.2 1.0
N2 B:RYS301 5.0 61.9 1.0

Fluorine binding site 6 out of 6 in 6w0n

Go back to Fluorine Binding Sites List in 6w0n
Fluorine binding site 6 out of 6 in the Structure of Khk in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Khk in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:75.5
occ:1.00
F3 B:RYS301 0.0 75.5 1.0
C15 B:RYS301 1.3 74.3 1.0
F2 B:RYS301 2.1 76.8 1.0
F1 B:RYS301 2.1 77.4 1.0
C8 B:RYS301 2.4 66.9 1.0
C16 B:RYS301 2.9 58.1 1.0
C7 B:RYS301 3.0 58.9 1.0
CD B:PRO247 3.2 51.2 1.0
N4 B:RYS301 3.3 58.4 1.0
C9 B:RYS301 3.4 66.4 1.0
CA B:PRO246 3.5 49.1 1.0
CB B:PRO246 3.8 50.7 1.0
CB B:CYS289 3.9 54.0 1.0
CG2 B:VAL250 4.0 61.3 1.0
SG B:CYS289 4.0 57.7 1.0
N B:PRO247 4.2 50.3 1.0
C6 B:RYS301 4.3 56.6 1.0
CG B:PRO247 4.3 55.4 1.0
N B:PRO246 4.5 49.0 1.0
C B:PRO246 4.5 53.5 1.0
C10 B:RYS301 4.6 68.4 1.0
CA B:GLY286 4.9 42.5 1.0
O B:PHE245 4.9 47.6 1.0
O B:GLY286 4.9 54.1 1.0
N2 B:RYS301 5.0 61.9 1.0

Reference:

K.Futatsugi, A.C.Smith, M.Tu, B.Raymer, K.Ahn, S.B.Coffey, M.S.Dowling, D.P.Fernando, J.A.Gutierrez, K.Huard, J.Jasti, A.S.Kalgutkar, J.D.Knafels, J.Pandit, K.D.Parris, S.Perez, J.A.Pfefferkorn, D.A.Price, T.Ryder, A.Shavnya, I.A.Stock, A.S.Tsai, G.J.Tesz, B.A.Thuma, Y.Weng, H.M.Wisniewska, G.Xing, J.Zhou, T.V.Magee. Discovery of Pf-06835919: A Potent Inhibitor of Ketohexokinase (Khk) For the Treatment of Metabolic Disorders Driven By the Overconsumption of Fructose. J.Med.Chem. V. 63 13546 2020.
ISSN: ISSN 0022-2623
PubMed: 32910646
DOI: 10.1021/ACS.JMEDCHEM.0C00944
Page generated: Sun Dec 13 13:25:27 2020

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