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Fluorine in PDB 4muk: Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid

Enzymatic activity of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid

All present enzymatic activity of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid:
6.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid, PDB code: 4muk was solved by H.L.Silvestre, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.58 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.620, 70.910, 81.810, 90.00, 99.51, 90.00
R / Rfree (%) 17.4 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid (pdb code 4muk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid, PDB code: 4muk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4muk

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Fluorine binding site 1 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.9
occ:0.50
 FAH A:2DV401 0.0 27.9 0.5
FAH A:2DV401 1.2 20.0 0.5
CBE A:2DV401 1.6 29.6 0.5
CBE A:2DV401 2.2 19.9 0.5
FAG A:2DV401 2.3 25.3 0.5
FAI A:2DV401 2.3 28.9 0.5
FAI A:2DV401 2.5 16.6 0.5
CAZ A:2DV401 2.5 29.7 0.5
CAL A:2DV401 2.7 19.3 0.5
CAL A:2DV401 2.7 29.6 0.5
CAZ A:2DV401 2.8 19.9 0.5
O A:HOH504 3.2 21.2 1.0
O A:PHE67 3.2 32.5 1.0
FAG A:2DV401 3.2 15.0 0.5
CG1 A:VAL142 3.7 20.4 1.0
CAM A:2DV401 3.8 29.6 0.5
CD1 A:LEU146 4.0 23.0 1.0
CAJ A:2DV401 4.0 21.3 0.5
CAJ A:2DV401 4.1 30.7 0.5
CAM A:2DV401 4.2 20.9 0.5
C A:PHE67 4.2 33.1 1.0
CD2 A:PHE67 4.3 30.2 1.0
O A:THR39 4.3 20.3 1.0
CB A:PHE67 4.4 29.1 1.0
CB A:VAL142 4.5 20.0 1.0
CE A:MET40 4.7 36.9 1.0
CA A:PHE67 4.8 29.4 1.0
CG A:PHE67 4.9 29.7 1.0
CG A:MET40 4.9 33.0 1.0
CAK A:2DV401 4.9 30.8 0.5

Fluorine binding site 2 out of 9 in 4muk

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Fluorine binding site 2 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:20.0
occ:0.50
 FAH A:2DV401 0.0 20.0 0.5
CBE A:2DV401 0.7 29.6 0.5
FAH A:2DV401 1.2 27.9 0.5
CBE A:2DV401 1.3 19.9 0.5
FAG A:2DV401 1.4 25.3 0.5
FAI A:2DV401 1.4 28.9 0.5
FAI A:2DV401 2.1 16.6 0.5
CAZ A:2DV401 2.1 29.7 0.5
FAG A:2DV401 2.1 15.0 0.5
CAZ A:2DV401 2.3 19.9 0.5
CAL A:2DV401 2.7 19.3 0.5
CAL A:2DV401 2.9 29.6 0.5
CAM A:2DV401 3.2 29.6 0.5
CG1 A:VAL142 3.6 20.4 1.0
CAM A:2DV401 3.6 20.9 0.5
O A:PHE67 3.9 32.5 1.0
CB A:VAL142 4.0 20.0 1.0
CAJ A:2DV401 4.1 21.3 0.5
CAJ A:2DV401 4.3 30.7 0.5
O A:HOH504 4.3 21.2 1.0
CE A:MET40 4.3 36.9 1.0
CAK A:2DV401 4.5 30.8 0.5
CD1 A:LEU146 4.6 23.0 1.0
CG2 A:VAL142 4.7 23.2 1.0
CAK A:2DV401 4.8 22.0 0.5
CD2 A:PHE67 4.8 30.2 1.0
CAX A:2DV401 4.9 30.5 0.5
CAX A:2DV401 5.0 22.3 0.5
C A:PHE67 5.0 33.1 1.0
CG A:MET40 5.0 33.0 1.0

Fluorine binding site 3 out of 9 in 4muk

Go back to Fluorine Binding Sites List in 4muk
Fluorine binding site 3 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:28.9
occ:0.50
 FAI A:2DV401 0.0 28.9 0.5
CBE A:2DV401 0.7 19.9 0.5
FAI A:2DV401 1.2 16.6 0.5
FAG A:2DV401 1.2 15.0 0.5
CBE A:2DV401 1.3 29.6 0.5
FAH A:2DV401 1.4 20.0 0.5
FAG A:2DV401 2.1 25.3 0.5
CAZ A:2DV401 2.1 19.9 0.5
CAZ A:2DV401 2.2 29.7 0.5
FAH A:2DV401 2.3 27.9 0.5
CAM A:2DV401 2.9 29.6 0.5
CAM A:2DV401 3.0 20.9 0.5
CAL A:2DV401 3.1 19.3 0.5
CAL A:2DV401 3.3 29.6 0.5
CB A:VAL142 3.5 20.0 1.0
CG1 A:VAL142 3.6 20.4 1.0
CG2 A:VAL143 3.8 15.8 1.0
O A:VAL139 4.1 17.9 1.0
N A:VAL143 4.1 16.2 1.0
CAK A:2DV401 4.2 30.8 0.5
CAK A:2DV401 4.3 22.0 0.5
C A:VAL142 4.4 17.2 1.0
CAJ A:2DV401 4.4 21.3 0.5
CAJ A:2DV401 4.4 30.7 0.5
CD1 A:LEU146 4.5 23.0 1.0
CG2 A:VAL142 4.5 23.2 1.0
CA A:VAL142 4.6 17.9 1.0
CA A:VAL143 4.6 17.3 1.0
CG1 A:VAL139 4.8 17.7 1.0
CB A:VAL143 4.8 16.6 1.0
CAX A:2DV401 4.8 30.5 0.5
CA A:VAL139 4.9 18.0 1.0
CAX A:2DV401 4.9 22.3 0.5
O A:VAL142 4.9 16.6 1.0
C A:VAL139 5.0 16.6 1.0

Fluorine binding site 4 out of 9 in 4muk

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Fluorine binding site 4 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:16.6
occ:0.50
 FAI A:2DV401 0.0 16.6 0.5
FAI A:2DV401 1.2 28.9 0.5
CBE A:2DV401 1.3 19.9 0.5
CBE A:2DV401 2.0 29.6 0.5
FAH A:2DV401 2.1 20.0 0.5
CAZ A:2DV401 2.2 19.9 0.5
FAG A:2DV401 2.2 15.0 0.5
FAH A:2DV401 2.5 27.9 0.5
CAZ A:2DV401 2.5 29.7 0.5
CAL A:2DV401 3.1 19.3 0.5
FAG A:2DV401 3.1 25.3 0.5
CAM A:2DV401 3.1 20.9 0.5
CAL A:2DV401 3.1 29.6 0.5
CAM A:2DV401 3.3 29.6 0.5
CG2 A:VAL143 3.4 15.8 1.0
CD1 A:LEU146 3.5 23.0 1.0
CG1 A:VAL142 3.7 20.4 1.0
N A:VAL143 3.8 16.2 1.0
CB A:VAL142 3.9 20.0 1.0
CA A:VAL143 3.9 17.3 1.0
C A:VAL142 4.1 17.2 1.0
CAJ A:2DV401 4.2 30.7 0.5
CB A:VAL143 4.3 16.6 1.0
CAJ A:2DV401 4.3 21.3 0.5
CAK A:2DV401 4.3 22.0 0.5
CAK A:2DV401 4.4 30.8 0.5
O A:VAL142 4.4 16.6 1.0
O A:VAL139 4.4 17.9 1.0
CG A:LEU146 4.5 20.5 1.0
O A:HOH504 4.5 21.2 1.0
CA A:VAL142 4.6 17.9 1.0
CAX A:2DV401 4.8 30.5 0.5
CB A:PRO38 4.8 19.3 1.0
CAX A:2DV401 4.8 22.3 0.5

Fluorine binding site 5 out of 9 in 4muk

Go back to Fluorine Binding Sites List in 4muk
Fluorine binding site 5 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:25.3
occ:0.50
 FAG A:2DV401 0.0 25.3 0.5
CBE A:2DV401 1.3 29.6 0.5
FAH A:2DV401 1.4 20.0 0.5
CBE A:2DV401 1.9 19.9 0.5
FAG A:2DV401 1.9 15.0 0.5
FAI A:2DV401 2.1 28.9 0.5
CAZ A:2DV401 2.2 29.7 0.5
FAH A:2DV401 2.3 27.9 0.5
CAZ A:2DV401 2.5 19.9 0.5
CAM A:2DV401 2.8 29.6 0.5
CAL A:2DV401 3.0 19.3 0.5
FAI A:2DV401 3.1 16.6 0.5
CE A:MET40 3.3 36.9 1.0
CAL A:2DV401 3.3 29.6 0.5
CAM A:2DV401 3.5 20.9 0.5
O A:PHE67 4.1 32.5 1.0
CAK A:2DV401 4.2 30.8 0.5
CAJ A:2DV401 4.2 21.3 0.5
SD A:MET40 4.3 44.3 1.0
CG1 A:VAL142 4.4 20.4 1.0
CG A:MET40 4.5 33.0 1.0
CAJ A:2DV401 4.5 30.7 0.5
CB A:VAL142 4.5 20.0 1.0
CAK A:2DV401 4.6 22.0 0.5
CB A:ASN69 4.8 51.1 1.0
N A:ASN69 4.8 46.9 1.0
CAX A:2DV401 4.9 30.5 0.5
CG2 A:VAL142 4.9 23.2 1.0
CAX A:2DV401 4.9 22.3 0.5

Fluorine binding site 6 out of 9 in 4muk

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Fluorine binding site 6 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:15.0
occ:0.50
 FAG A:2DV401 0.0 15.0 0.5
FAI A:2DV401 1.2 28.9 0.5
CBE A:2DV401 1.3 19.9 0.5
CBE A:2DV401 1.8 29.6 0.5
FAG A:2DV401 1.9 25.3 0.5
FAH A:2DV401 2.1 20.0 0.5
FAI A:2DV401 2.2 16.6 0.5
CAZ A:2DV401 2.3 19.9 0.5
CAZ A:2DV401 2.4 29.7 0.5
CAM A:2DV401 2.5 29.6 0.5
CAM A:2DV401 2.8 20.9 0.5
FAH A:2DV401 3.2 27.9 0.5
CAL A:2DV401 3.5 19.3 0.5
O A:VAL139 3.7 17.9 1.0
CAL A:2DV401 3.7 29.6 0.5
CG1 A:VAL139 3.8 17.7 1.0
CAK A:2DV401 3.9 30.8 0.5
CB A:VAL142 3.9 20.0 1.0
CA A:VAL139 4.0 18.0 1.0
CG2 A:VAL143 4.0 15.8 1.0
CAK A:2DV401 4.1 22.0 0.5
C A:VAL139 4.3 16.6 1.0
CB A:VAL139 4.3 18.5 1.0
CG1 A:VAL142 4.3 20.4 1.0
CG2 A:VAL139 4.5 19.9 1.0
N A:VAL143 4.5 16.2 1.0
CAJ A:2DV401 4.6 21.3 0.5
CG2 A:VAL142 4.7 23.2 1.0
CAJ A:2DV401 4.7 30.7 0.5
CAX A:2DV401 4.8 30.5 0.5
CE A:MET40 4.9 36.9 1.0
CAX A:2DV401 4.9 22.3 0.5
C A:VAL142 5.0 17.2 1.0
CA A:VAL142 5.0 17.9 1.0

Fluorine binding site 7 out of 9 in 4muk

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Fluorine binding site 7 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:38.5
occ:1.00
 FAH B:2DV401 0.0 38.5 1.0
CBE B:2DV401 1.3 33.9 1.0
FAI B:2DV401 2.0 33.5 1.0
FAG B:2DV401 2.0 33.8 1.0
CAZ B:2DV401 2.3 26.5 1.0
CAM B:2DV401 2.8 29.4 1.0
CAL B:2DV401 3.6 24.2 1.0
O B:HOH676 4.1 46.7 1.0
CE B:MET40 4.1 47.5 1.0
CA B:VAL139 4.1 17.7 1.0
CAK B:2DV401 4.2 27.0 1.0
CG2 B:VAL139 4.2 20.2 1.0
CB B:VAL142 4.3 18.1 1.0
CG1 B:VAL139 4.4 17.3 1.0
CB B:VAL139 4.5 17.8 1.0
SD B:MET40 4.5 50.6 1.0
CG1 B:VAL142 4.5 20.2 1.0
CG B:MET40 4.6 39.1 1.0
O B:VAL139 4.6 19.2 1.0
CG2 B:VAL142 4.7 20.4 1.0
CAJ B:2DV401 4.7 22.6 1.0
C B:VAL139 4.9 17.6 1.0
CAX B:2DV401 5.0 24.3 1.0
N B:VAL139 5.0 17.9 1.0

Fluorine binding site 8 out of 9 in 4muk

Go back to Fluorine Binding Sites List in 4muk
Fluorine binding site 8 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.5
occ:1.00
 FAI B:2DV401 0.0 33.5 1.0
CBE B:2DV401 1.2 33.9 1.0
FAH B:2DV401 2.0 38.5 1.0
FAG B:2DV401 2.0 33.8 1.0
CAZ B:2DV401 2.2 26.5 1.0
CAL B:2DV401 2.8 24.2 1.0
CAM B:2DV401 3.5 29.4 1.0
CG1 B:VAL142 3.8 20.2 1.0
CG B:MET40 3.9 39.1 1.0
CAJ B:2DV401 4.2 22.6 1.0
O B:HOH526 4.2 21.0 1.0
CB B:VAL142 4.2 18.1 1.0
CD2 B:PHE67 4.3 45.2 1.0
SD B:MET40 4.6 50.6 1.0
CB B:PHE67 4.7 42.8 1.0
CAK B:2DV401 4.7 27.0 1.0
CE B:MET40 4.7 47.5 1.0
CG2 B:VAL142 4.8 20.4 1.0
CG B:PHE67 4.9 47.0 1.0
CD1 B:LEU146 4.9 22.1 1.0
CAX B:2DV401 4.9 24.3 1.0

Fluorine binding site 9 out of 9 in 4muk

Go back to Fluorine Binding Sites List in 4muk
Fluorine binding site 9 out of 9 in the Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Pantothenate Synthetase in Complex with 2-(5- Methoxy-2-(4-(Trifluoromethyl)Benzylsulfonylcarbamoyl)-1H-Indol-1- Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.8
occ:1.00
 FAG B:2DV401 0.0 33.8 1.0
CBE B:2DV401 1.3 33.9 1.0
FAH B:2DV401 2.0 38.5 1.0
FAI B:2DV401 2.0 33.5 1.0
CAZ B:2DV401 2.2 26.5 1.0
CAM B:2DV401 3.0 29.4 1.0
CAL B:2DV401 3.1 24.2 1.0
CG2 B:VAL143 3.5 17.2 1.0
CB B:VAL142 3.6 18.1 1.0
CG1 B:VAL142 3.7 20.2 1.0
O B:VAL139 3.9 19.2 1.0
N B:VAL143 4.0 16.1 1.0
CAK B:2DV401 4.3 27.0 1.0
CAJ B:2DV401 4.3 22.6 1.0
C B:VAL142 4.3 14.9 1.0
CG1 B:VAL139 4.5 17.3 1.0
CA B:VAL143 4.5 16.6 1.0
CA B:VAL139 4.6 17.7 1.0
CA B:VAL142 4.6 16.3 1.0
CD1 B:LEU146 4.6 22.1 1.0
CB B:VAL143 4.7 16.7 1.0
C B:VAL139 4.7 17.6 1.0
CG2 B:VAL142 4.7 20.4 1.0
CAX B:2DV401 4.8 24.3 1.0
O B:VAL142 5.0 16.0 1.0
CB B:VAL139 5.0 17.8 1.0

Reference:

A.W.Hung, H.L Silvestre, S.Wen, J.Boland, T.L.Blundell, A.Ciulli, C.Abell. Group Efficiency Analysis As A Tool For Optimization of Fragment-Based Approaches To Be Published.
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