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Fluorine in PDB 6w0y: Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)

Enzymatic activity of Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)

All present enzymatic activity of Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid):
2.7.1.3;

Protein crystallography data

The structure of Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid), PDB code: 6w0y was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.972, 83.556, 137.595, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) (pdb code 6w0y). 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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid), PDB code: 6w0y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 1 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:81.6
occ:1.00
 F1 A:S6S301 0.0 81.6 1.0
C17 A:S6S301 1.3 77.2 1.0
F2 A:S6S301 2.1 79.8 1.0
F3 A:S6S301 2.1 78.0 1.0
C7 A:S6S301 2.3 70.4 1.0
C18 A:S6S301 2.7 64.2 1.0
C6 A:S6S301 2.9 64.7 1.0
N4 A:S6S301 3.2 63.8 1.0
CA A:PRO246 3.4 46.2 1.0
CD A:PRO247 3.4 52.2 1.0
C8 A:S6S301 3.5 67.9 1.0
SG A:CYS289 3.7 57.4 1.0
CB A:CYS289 3.7 54.2 1.0
CA A:GLY286 3.9 45.7 1.0
CB A:PRO246 3.9 45.8 1.0
N A:PRO246 4.1 46.9 1.0
C5 A:S6S301 4.2 63.7 1.0
O A:PHE245 4.2 52.3 1.0
N A:PRO247 4.3 50.5 1.0
O A:GLY286 4.3 51.5 1.0
C A:PRO246 4.4 52.6 1.0
C A:PHE245 4.4 52.1 1.0
C A:GLY286 4.6 50.6 1.0
CG A:PRO247 4.6 56.5 1.0
C9 A:S6S301 4.6 66.2 1.0
N A:GLY286 4.7 46.9 1.0
CD A:PRO246 4.9 45.6 1.0
O A:ALA285 4.9 54.7 1.0
N2 A:S6S301 4.9 65.2 1.0

Fluorine binding site 2 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 2 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:79.8
occ:1.00
 F2 A:S6S301 0.0 79.8 1.0
C17 A:S6S301 1.3 77.2 1.0
F1 A:S6S301 2.1 81.6 1.0
F3 A:S6S301 2.1 78.0 1.0
C7 A:S6S301 2.4 70.4 1.0
C8 A:S6S301 2.7 67.9 1.0
C6 A:S6S301 3.6 64.7 1.0
SG A:CYS289 3.6 57.4 1.0
CB A:CYS289 3.8 54.2 1.0
CG1 A:VAL250 4.0 57.2 1.0
CG2 A:VAL250 4.0 55.1 1.0
C9 A:S6S301 4.1 66.2 1.0
C18 A:S6S301 4.2 64.2 1.0
CD A:PRO247 4.2 52.2 1.0
CG2 A:THR253 4.6 49.3 1.0
CB A:VAL250 4.6 56.5 1.0
C5 A:S6S301 4.7 63.7 1.0
CB A:PRO246 4.7 45.8 1.0
CA A:PRO246 4.7 46.2 1.0
CB A:GLU227 4.8 62.1 1.0
OE2 A:GLU227 4.9 96.3 1.0
N2 A:S6S301 4.9 65.2 1.0
N3 A:S6S301 4.9 64.4 1.0
N4 A:S6S301 5.0 63.8 1.0
C10 A:S6S301 5.0 63.5 1.0

Fluorine binding site 3 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 3 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:78.0
occ:1.00
 F3 A:S6S301 0.0 78.0 1.0
C17 A:S6S301 1.3 77.2 1.0
F2 A:S6S301 2.1 79.8 1.0
F1 A:S6S301 2.1 81.6 1.0
C7 A:S6S301 2.3 70.4 1.0
C6 A:S6S301 3.2 64.7 1.0
C8 A:S6S301 3.2 67.9 1.0
CB A:GLU227 3.3 62.1 1.0
C18 A:S6S301 3.3 64.2 1.0
CB A:PRO246 3.6 45.8 1.0
CA A:GLU227 3.7 60.1 1.0
CA A:PRO246 3.8 46.2 1.0
N4 A:S6S301 3.9 63.8 1.0
N A:GLU227 4.3 59.6 1.0
C5 A:S6S301 4.4 63.7 1.0
N A:PRO246 4.4 46.9 1.0
C9 A:S6S301 4.5 66.2 1.0
CG A:PRO246 4.5 48.8 1.0
CG A:GLU227 4.5 76.4 1.0
CD A:PRO246 4.6 45.6 1.0
CB A:ALA244 4.6 47.7 1.0
OE2 A:GLU227 4.6 96.3 1.0
CD A:PRO247 4.7 52.2 1.0
C A:GLU227 4.9 63.2 1.0
N2 A:S6S301 4.9 65.2 1.0
C A:ALA226 5.0 63.2 1.0

Fluorine binding site 4 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 4 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:85.2
occ:1.00
 F1 B:S6S301 0.0 85.2 1.0
C17 B:S6S301 1.3 80.9 1.0
F2 B:S6S301 2.1 84.5 1.0
F3 B:S6S301 2.2 79.2 1.0
C7 B:S6S301 2.4 71.9 1.0
C8 B:S6S301 2.7 65.8 1.0
SG B:CYS289 3.5 64.5 1.0
C6 B:S6S301 3.6 64.7 1.0
CB B:CYS289 3.7 61.2 1.0
CG2 B:VAL250 3.9 69.0 1.0
CD B:PRO247 4.1 61.0 1.0
C9 B:S6S301 4.1 64.0 1.0
C18 B:S6S301 4.2 59.4 1.0
CG2 B:THR253 4.6 64.4 1.0
CB B:PRO246 4.7 59.9 1.0
CA B:PRO246 4.7 58.9 1.0
C5 B:S6S301 4.7 64.2 1.0
OE1 B:GLU227 4.8 74.3 1.0
CB B:GLU227 4.8 62.7 1.0
N2 B:S6S301 4.9 63.4 1.0
CG1 B:VAL250 4.9 68.7 1.0
CG B:PRO247 4.9 66.2 1.0
N3 B:S6S301 4.9 65.3 1.0
C10 B:S6S301 5.0 64.8 1.0
N4 B:S6S301 5.0 57.0 1.0

Fluorine binding site 5 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 5 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:84.5
occ:1.00
 F2 B:S6S301 0.0 84.5 1.0
C17 B:S6S301 1.3 80.9 1.0
F1 B:S6S301 2.1 85.2 1.0
F3 B:S6S301 2.1 79.2 1.0
C7 B:S6S301 2.4 71.9 1.0
C18 B:S6S301 2.7 59.4 1.0
C6 B:S6S301 2.8 64.7 1.0
N4 B:S6S301 3.1 57.0 1.0
CA B:PRO246 3.3 58.9 1.0
CD B:PRO247 3.4 61.0 1.0
C8 B:S6S301 3.5 65.8 1.0
SG B:CYS289 3.7 64.5 1.0
CA B:GLY286 3.8 51.5 1.0
CB B:CYS289 3.8 61.2 1.0
CB B:PRO246 3.9 59.9 1.0
N B:PRO246 4.0 60.1 1.0
C5 B:S6S301 4.2 64.2 1.0
N B:PRO247 4.2 61.0 1.0
O B:PHE245 4.3 60.9 1.0
C B:PRO246 4.3 63.0 1.0
O B:GLY286 4.3 55.7 1.0
C B:PHE245 4.4 62.3 1.0
C B:GLY286 4.6 56.0 1.0
CG B:PRO247 4.6 66.2 1.0
N B:GLY286 4.7 51.5 1.0
C9 B:S6S301 4.7 64.0 1.0
CD B:PRO246 4.7 60.7 1.0
O B:ALA285 4.8 53.1 1.0
N2 B:S6S301 4.9 63.4 1.0

Fluorine binding site 6 out of 6 in 6w0y

Go back to Fluorine Binding Sites List in 6w0y
Fluorine binding site 6 out of 6 in the Structure of Khk in Complex with Compound 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid)


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 6 (2-[(1~{R},5~{S})-3-[5- Cyano-6-[(2~{S},3~{R})-2-Methyl-3-Oxidanyl-Azetidin-1-Yl]-4- (Trifluoromethyl)Pyridin-2-Yl]-3-Azabicyclo[3.1.0]Hexan-6-Yl]Ethanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:79.2
occ:1.00
 F3 B:S6S301 0.0 79.2 1.0
C17 B:S6S301 1.3 80.9 1.0
F2 B:S6S301 2.1 84.5 1.0
F1 B:S6S301 2.2 85.2 1.0
C7 B:S6S301 2.4 71.9 1.0
C6 B:S6S301 3.2 64.7 1.0
C8 B:S6S301 3.3 65.8 1.0
CB B:GLU227 3.3 62.7 1.0
C18 B:S6S301 3.4 59.4 1.0
CB B:PRO246 3.6 59.9 1.0
CA B:GLU227 3.7 60.0 1.0
CA B:PRO246 3.9 58.9 1.0
N4 B:S6S301 3.9 57.0 1.0
O B:HOH497 4.1 68.0 1.0
N B:GLU227 4.3 58.0 1.0
N B:PRO246 4.4 60.1 1.0
C5 B:S6S301 4.4 64.2 1.0
C9 B:S6S301 4.5 64.0 1.0
CB B:ALA244 4.5 52.1 1.0
CD B:PRO246 4.5 60.7 1.0
CG B:GLU227 4.5 79.1 1.0
OE1 B:GLU227 4.5 74.3 1.0
CG B:PRO246 4.6 63.8 1.0
CD B:PRO247 4.7 61.0 1.0
C B:GLU227 4.9 62.7 1.0
N2 B:S6S301 5.0 63.4 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: Tue Jul 15 16:56:18 2025

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