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Fluorine in PDB 6b7e: Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One

Enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One

All present enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One, PDB code: 6b7e was solved by A.W.Proudfoot, D.Bussiere, A.Lingel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.29 / 2.10
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 135.480, 135.480, 135.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One (pdb code 6b7e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One, PDB code: 6b7e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6b7e

Go back to Fluorine Binding Sites List in 6b7e
Fluorine binding site 1 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One


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 E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:51.0
occ:1.00
 F20 B:CWA201 0.0 51.0 1.0
C19 B:CWA201 1.4 44.2 1.0
F21 B:CWA201 2.3 45.2 1.0
C18 B:CWA201 2.4 34.5 1.0
O4 B:SO4205 2.5 66.6 1.0
O B:HOH397 2.9 47.7 1.0
N14 B:CWA201 3.0 31.2 1.0
C10 B:CWA201 3.2 25.6 1.0
C17 B:CWA201 3.4 31.6 1.0
S B:SO4205 3.8 62.5 1.0
C15 B:CWA201 4.1 32.8 1.0
O2 B:SO4205 4.2 63.5 1.0
C5 B:CWA201 4.2 23.9 1.0
C12 B:CWA201 4.2 28.4 1.0
C9 B:CWA201 4.2 27.8 1.0
CD2 B:LEU102 4.2 30.2 0.3
C4 B:CWA201 4.3 23.0 1.0
N16 B:CWA201 4.3 32.9 1.0
CD1 B:LEU102 4.4 30.3 0.7
O1 B:SO4205 4.4 64.6 1.0
NH1 B:ARG88 4.5 34.6 1.0
NH2 B:ARG88 4.5 37.3 1.0
CZ B:ARG88 4.8 35.7 1.0
O3 B:SO4205 4.8 61.0 1.0

Fluorine binding site 2 out of 2 in 6b7e

Go back to Fluorine Binding Sites List in 6b7e
Fluorine binding site 2 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One


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 E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-4-(5-(Difluoromethyl)-1H-Imidazol-1- Yl)-3,3-Dimethylisochroman-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:45.2
occ:1.00
 F21 B:CWA201 0.0 45.2 1.0
C19 B:CWA201 1.4 44.2 1.0
C18 B:CWA201 2.3 34.5 1.0
F20 B:CWA201 2.3 51.0 1.0
C17 B:CWA201 2.7 31.6 1.0
O4 B:SO4205 2.9 66.6 1.0
NH1 B:ARG88 3.3 34.6 1.0
CA B:GLY9 3.4 21.6 1.0
N14 B:CWA201 3.5 31.2 1.0
N B:GLY9 3.5 21.3 1.0
C B:PRO8 3.7 21.1 1.0
O B:PRO8 3.8 21.5 1.0
CB B:PRO8 4.0 21.2 1.0
CZ B:ARG88 4.0 35.7 1.0
N16 B:CWA201 4.1 32.9 1.0
C12 B:CWA201 4.1 28.4 1.0
C10 B:CWA201 4.2 25.6 1.0
S B:SO4205 4.2 62.5 1.0
C B:GLY9 4.3 21.5 1.0
CG B:PRO8 4.3 21.1 1.0
C15 B:CWA201 4.4 32.8 1.0
NH2 B:ARG88 4.5 37.3 1.0
CA B:PRO8 4.5 21.3 1.0
O3 B:SO4205 4.5 61.0 1.0
O B:HOH397 4.7 47.7 1.0
N B:THR10 4.8 20.6 1.0
C9 B:CWA201 4.9 27.8 1.0
NE B:ARG88 4.9 34.4 1.0
O B:GLY9 4.9 22.2 1.0
CB B:ALA37 5.0 20.8 1.0

Reference:

A.Proudfoot, D.E.Bussiere, A.Lingel. High-Confidence Protein-Ligand Complex Modeling By uc(Nmr)-Guided Docking Enables Early Hit Optimization. J. Am. Chem. Soc. V. 139 17824 2017.
ISSN: ESSN 1520-5126
PubMed: 29190085
DOI: 10.1021/JACS.7B07171
Page generated: Tue Jul 15 09:58:12 2025

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