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Fluorine in PDB 6w0x: Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)

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

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

Protein crystallography data

The structure of Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile), PDB code: 6w0x was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.94 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.790, 85.820, 137.760, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile) (pdb code 6w0x). 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 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile), PDB code: 6w0x:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w0x

Go back to Fluorine Binding Sites List in 6w0x
Fluorine binding site 1 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:75.8
occ:1.00
 F26 A:S6J301 0.0 75.8 1.0
C25 A:S6J301 1.3 72.3 1.0
F27 A:S6J301 2.1 72.2 1.0
F28 A:S6J301 2.2 71.4 1.0
C10 A:S6J301 2.4 65.7 1.0
C9 A:S6J301 3.0 61.4 1.0
C29 A:S6J301 3.1 60.5 1.0
CB A:PRO246 3.4 46.4 1.0
CB A:GLU227 3.4 59.3 1.0
C11 A:S6J301 3.4 64.7 1.0
N30 A:S6J301 3.6 58.2 1.0
CA A:PRO246 3.6 45.8 1.0
CA A:GLU227 3.8 57.8 1.0
N A:PRO246 4.2 45.6 1.0
CG A:PRO246 4.3 49.6 1.0
C8 A:S6J301 4.3 61.2 1.0
CD A:PRO246 4.3 46.1 1.0
CB A:ALA244 4.4 46.7 1.0
N A:GLU227 4.5 58.3 1.0
CG A:GLU227 4.5 73.7 1.0
C12 A:S6J301 4.6 66.3 1.0
CD A:PRO247 4.8 49.0 1.0
N13 A:S6J301 4.9 66.5 1.0
CG2 A:VAL250 5.0 54.1 1.0
C A:PRO246 5.0 48.8 1.0
C A:GLU227 5.0 61.3 1.0

Fluorine binding site 2 out of 6 in 6w0x

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Fluorine binding site 2 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:72.2
occ:1.00
 F27 A:S6J301 0.0 72.2 1.0
C25 A:S6J301 1.3 72.3 1.0
F26 A:S6J301 2.1 75.8 1.0
F28 A:S6J301 2.2 71.4 1.0
C10 A:S6J301 2.4 65.7 1.0
C11 A:S6J301 2.7 64.7 1.0
CG2 A:VAL250 3.6 54.1 1.0
C9 A:S6J301 3.7 61.4 1.0
CG1 A:VAL250 4.0 54.1 1.0
C12 A:S6J301 4.1 66.3 1.0
SG A:CYS289 4.3 58.0 1.0
C29 A:S6J301 4.3 60.5 1.0
CB A:CYS289 4.3 54.0 1.0
CB A:GLU227 4.4 59.3 1.0
CB A:VAL250 4.5 54.6 1.0
CD A:PRO247 4.6 49.0 1.0
CB A:PRO246 4.6 46.4 1.0
C8 A:S6J301 4.8 61.2 1.0
CA A:PRO246 4.8 45.8 1.0
N13 A:S6J301 4.9 66.5 1.0
N14 A:S6J301 5.0 71.1 1.0
C15 A:S6J301 5.0 70.8 1.0

Fluorine binding site 3 out of 6 in 6w0x

Go back to Fluorine Binding Sites List in 6w0x
Fluorine binding site 3 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:71.4
occ:1.00
 F28 A:S6J301 0.0 71.4 1.0
C25 A:S6J301 1.4 72.3 1.0
F27 A:S6J301 2.2 72.2 1.0
F26 A:S6J301 2.2 75.8 1.0
C10 A:S6J301 2.4 65.7 1.0
C29 A:S6J301 2.9 60.5 1.0
C9 A:S6J301 3.0 61.4 1.0
CD A:PRO247 3.3 49.0 1.0
N30 A:S6J301 3.4 58.2 1.0
C11 A:S6J301 3.5 64.7 1.0
CA A:PRO246 3.5 45.8 1.0
CB A:CYS289 3.6 54.0 1.0
SG A:CYS289 3.7 58.0 1.0
CA A:GLY286 3.9 45.6 1.0
CB A:PRO246 4.0 46.4 1.0
N A:PRO247 4.3 48.3 1.0
O A:GLY286 4.3 51.0 1.0
N A:PRO246 4.3 45.6 1.0
C8 A:S6J301 4.4 61.2 1.0
CG2 A:VAL250 4.4 54.1 1.0
C A:PRO246 4.4 48.8 1.0
O A:PHE245 4.5 46.2 1.0
CG A:PRO247 4.5 53.7 1.0
C A:GLY286 4.6 50.8 1.0
C12 A:S6J301 4.6 66.3 1.0
C A:PHE245 4.7 48.3 1.0
N A:GLY286 4.8 45.2 1.0
O A:ALA285 4.9 54.1 1.0
CA A:CYS289 5.0 53.6 1.0
N13 A:S6J301 5.0 66.5 1.0

Fluorine binding site 4 out of 6 in 6w0x

Go back to Fluorine Binding Sites List in 6w0x
Fluorine binding site 4 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:75.6
occ:1.00
 F26 B:S6J301 0.0 75.6 1.0
C25 B:S6J301 1.3 69.0 1.0
F27 B:S6J301 2.1 69.3 1.0
F28 B:S6J301 2.2 72.5 1.0
C10 B:S6J301 2.4 58.9 1.0
C11 B:S6J301 2.7 53.5 1.0
OE1 B:GLU227 3.6 71.8 1.0
C9 B:S6J301 3.7 51.6 1.0
CG2 B:VAL250 3.9 66.9 1.0
C12 B:S6J301 4.1 53.4 1.0
CB B:GLU227 4.2 56.4 1.0
CD B:PRO247 4.2 54.6 1.0
C29 B:S6J301 4.3 52.5 1.0
SG B:CYS289 4.3 59.0 1.0
CB B:CYS289 4.4 54.5 1.0
CD B:GLU227 4.5 91.2 1.0
CB B:PRO246 4.5 54.0 1.0
CA B:PRO246 4.6 52.6 1.0
CG B:GLU227 4.8 74.9 1.0
C8 B:S6J301 4.8 49.9 1.0
O B:HOH587 4.8 66.6 1.0
CA B:GLU227 4.9 53.4 1.0
C15 B:S6J301 4.9 58.2 1.0
N13 B:S6J301 4.9 49.7 1.0
CG1 B:VAL250 5.0 67.3 1.0
N14 B:S6J301 5.0 58.4 1.0

Fluorine binding site 5 out of 6 in 6w0x

Go back to Fluorine Binding Sites List in 6w0x
Fluorine binding site 5 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:69.3
occ:1.00
 F27 B:S6J301 0.0 69.3 1.0
C25 B:S6J301 1.3 69.0 1.0
F26 B:S6J301 2.1 75.6 1.0
F28 B:S6J301 2.1 72.5 1.0
C10 B:S6J301 2.4 58.9 1.0
C29 B:S6J301 3.0 52.5 1.0
C9 B:S6J301 3.0 51.6 1.0
CD B:PRO247 3.1 54.6 1.0
C11 B:S6J301 3.4 53.5 1.0
N30 B:S6J301 3.4 56.3 1.0
CA B:PRO246 3.5 52.6 1.0
CB B:CYS289 3.6 54.5 1.0
SG B:CYS289 3.7 59.0 1.0
CA B:GLY286 3.9 48.1 1.0
N B:PRO247 4.1 54.9 1.0
CB B:PRO246 4.1 54.0 1.0
CG B:PRO247 4.2 58.9 1.0
O B:GLY286 4.3 51.5 1.0
N B:PRO246 4.3 52.4 1.0
C8 B:S6J301 4.3 49.9 1.0
O B:PHE245 4.3 53.7 1.0
C B:PRO246 4.4 57.5 1.0
C12 B:S6J301 4.6 53.4 1.0
C B:GLY286 4.6 54.0 1.0
C B:PHE245 4.6 53.1 1.0
CG2 B:VAL250 4.8 66.9 1.0
N B:GLY286 4.8 46.8 1.0
O B:ALA285 4.9 48.6 1.0
N13 B:S6J301 4.9 49.7 1.0

Fluorine binding site 6 out of 6 in 6w0x

Go back to Fluorine Binding Sites List in 6w0x
Fluorine binding site 6 out of 6 in the Structure of Khk in Complex with Compound 4 (6-[(1~{S},5~{R})-6- (Hydroxymethyl)-3-Azabicyclo[3.1.0]Hexan-3-Yl]-2-[(2~{S},3~{R})-2- Methyl-3-Oxidanyl-Azetidin-1-Yl]-4-(Trifluoromethyl)Pyridine-3- Carbonitrile)


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

b:72.5
occ:1.00
 F28 B:S6J301 0.0 72.5 1.0
C25 B:S6J301 1.3 69.0 1.0
F27 B:S6J301 2.1 69.3 1.0
F26 B:S6J301 2.2 75.6 1.0
C10 B:S6J301 2.4 58.9 1.0
C9 B:S6J301 3.0 51.6 1.0
C29 B:S6J301 3.0 52.5 1.0
CB B:PRO246 3.4 54.0 1.0
C11 B:S6J301 3.5 53.5 1.0
CB B:GLU227 3.5 56.4 1.0
N30 B:S6J301 3.5 56.3 1.0
CA B:PRO246 3.5 52.6 1.0
CA B:GLU227 3.8 53.4 1.0
N B:PRO246 3.9 52.4 1.0
O B:HOH475 4.0 57.8 1.0
CB B:ALA244 4.1 53.2 1.0
O B:HOH587 4.2 66.6 1.0
CD B:PRO246 4.2 54.7 1.0
CG B:PRO246 4.3 58.3 1.0
C8 B:S6J301 4.3 49.9 1.0
CD B:PRO247 4.5 54.6 1.0
OE1 B:GLU227 4.5 71.8 1.0
N B:GLU227 4.6 52.2 1.0
C12 B:S6J301 4.6 53.4 1.0
CG B:GLU227 4.6 74.9 1.0
C B:PHE245 4.7 53.1 1.0
C B:PRO246 4.9 57.5 1.0
C B:GLU227 4.9 54.4 1.0
CD B:GLU227 4.9 91.2 1.0
O B:GLU227 4.9 52.2 1.0
O B:PHE245 5.0 53.7 1.0
N13 B:S6J301 5.0 49.7 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: Fri Aug 2 03:19:25 2024

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