Fluorine in PDB 8szm: Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12

All present enzymatic activity of Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12:
3.4.21.92;

The structure of Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12, PDB code: 8szm was solved by M.F.Mabanglo, W.A.Houry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.83 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.968, 187.589, 169.408, 90, 93.72, 90
R / Rfree (%)	20.4 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 (pdb code 8szm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 27 binding sites of Fluorine where determined in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12, PDB code: 8szm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:77.7 occ:1.00 F08 G:X3O301 0.0 77.7 1.0 C07 G:X3O301 1.4 76.1 1.0 F10 G:X3O301 2.2 77.0 1.0 F09 G:X3O301 2.2 76.9 1.0 C06 G:X3O301 2.4 76.8 1.0 CE2 G:TYR76 3.0 54.9 1.0 C11 G:X3O301 3.3 77.5 1.0 C05 G:X3O301 3.3 80.1 1.0 OH G:TYR76 3.7 61.5 1.0 CZ G:TYR76 3.8 55.1 1.0 CD1 G:LEU128 3.8 48.5 0.9 CD2 G:TYR76 3.9 48.7 1.0 OG1 A:THR93 4.1 44.6 1.0 N12 G:X3O301 4.5 80.0 1.0 C04 G:X3O301 4.5 80.5 1.0 CD2 A:LEU62 4.6 51.6 1.0 CG G:LEU128 4.7 45.5 1.0 CG2 G:ILE104 4.7 47.0 1.0 CD2 G:LEU128 4.7 48.5 1.0 CD1 A:LEU62 4.7 49.2 1.0 SD G:MET106 4.9 49.4 1.0 CB A:THR93 4.9 41.0 1.0 CD2 A:PHE96 4.9 59.6 1.0 CG1 A:VAL58 5.0 42.5 1.0 CA A:THR93 5.0 46.1 1.0 C03 G:X3O301 5.0 82.1 1.0

Fluorine binding site 2 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:76.9 occ:1.00 F09 G:X3O301 0.0 76.9 1.0 C07 G:X3O301 1.4 76.1 1.0 F10 G:X3O301 2.2 77.0 1.0 F08 G:X3O301 2.2 77.7 1.0 C06 G:X3O301 2.4 76.8 1.0 C11 G:X3O301 2.9 77.5 1.0 CD2 A:PHE96 2.9 59.6 1.0 CG A:PHE96 3.1 55.4 1.0 CB A:PHE96 3.3 53.3 1.0 C05 G:X3O301 3.6 80.1 1.0 CE2 A:PHE96 3.7 64.8 1.0 CD1 A:PHE96 4.0 57.7 1.0 CD1 G:LEU128 4.1 48.5 0.9 CA A:THR93 4.1 46.1 1.0 N12 G:X3O301 4.2 80.0 1.0 OG1 A:THR93 4.4 44.6 1.0 CZ A:PHE96 4.5 62.6 1.0 CD2 A:LEU62 4.5 51.6 1.0 CG2 A:THR93 4.6 37.0 1.0 O A:THR93 4.6 47.6 1.0 CG2 A:ILE97 4.6 50.9 1.0 CE1 A:PHE96 4.6 55.3 1.0 CB A:THR93 4.6 41.0 1.0 CA A:PHE96 4.7 55.4 1.0 O A:ASP92 4.7 50.8 1.0 C04 G:X3O301 4.8 80.5 1.0 C A:THR93 4.9 46.3 1.0 N A:ILE97 4.9 49.8 1.0 N A:THR93 4.9 41.7 1.0 C03 G:X3O301 5.0 82.1 1.0 CD2 G:LEU128 5.0 48.5 1.0 OH G:TYR76 5.0 61.5 1.0

Fluorine binding site 3 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:77.0 occ:1.00 F10 G:X3O301 0.0 77.0 1.0 C07 G:X3O301 1.4 76.1 1.0 F09 G:X3O301 2.2 76.9 1.0 F08 G:X3O301 2.2 77.7 1.0 C06 G:X3O301 2.4 76.8 1.0 C05 G:X3O301 2.8 80.1 1.0 CD2 G:LEU128 3.1 48.5 1.0 CD1 G:LEU128 3.2 48.5 0.9 C11 G:X3O301 3.6 77.5 1.0 CG G:LEU128 3.6 45.5 1.0 CD1 G:LEU203 3.7 57.4 1.0 CG A:PHE96 3.8 55.4 1.0 CD1 A:PHE96 4.0 57.7 1.0 CD2 A:PHE96 4.0 59.6 1.0 CG2 G:ILE104 4.1 47.0 1.0 C04 G:X3O301 4.1 80.5 1.0 CB A:PHE96 4.3 53.3 1.0 CE1 A:PHE96 4.3 55.3 1.0 CE2 A:PHE96 4.3 64.8 1.0 CE2 G:TYR76 4.5 54.9 1.0 CZ A:PHE96 4.5 62.6 1.0 CB G:LEU203 4.6 43.3 1.0 N12 G:X3O301 4.7 80.0 1.0 CG G:LEU203 4.8 53.3 1.0 OH G:TYR76 4.9 61.5 1.0 C03 G:X3O301 4.9 82.1 1.0

Fluorine binding site 4 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:86.9 occ:1.00 F22 G:X3O301 0.0 86.9 1.0 C21 G:X3O301 1.4 90.7 1.0 F24 G:X3O301 2.2 87.0 1.0 F23 G:X3O301 2.2 80.9 1.0 C20 G:X3O301 2.4 90.7 1.0 C25 G:X3O301 2.8 82.3 1.0 NH2 G:ARG36 3.0 81.6 1.0 NE G:ARG36 3.4 77.3 1.0 CZ G:ARG36 3.4 80.7 1.0 CD1 A:PHE63 3.5 63.1 1.0 CB A:ALA66 3.6 59.4 1.0 CE1 A:PHE63 3.7 63.3 1.0 C19 G:X3O301 3.7 88.0 1.0 C26 G:X3O301 4.1 84.0 1.0 NH1 G:ARG36 4.3 79.0 1.0 O A:PHE63 4.3 57.3 1.0 CG G:ARG36 4.4 66.8 1.0 CD G:ARG36 4.4 69.5 1.0 OE2 G:GLU40 4.4 74.4 1.0 CG A:PHE63 4.6 56.0 1.0 N A:GLU67 4.6 65.2 1.0 S18 G:X3O301 4.6 102.4 1.0 CG A:GLU67 4.7 65.3 1.0 CA A:PHE63 4.7 56.7 1.0 C A:ALA66 4.7 59.1 1.0 C28 G:X3O301 4.8 80.0 1.0 CA A:ALA66 4.8 57.8 1.0 CZ A:PHE63 4.9 55.8 1.0 CD G:GLU40 4.9 80.2 1.0 C27 G:X3O301 5.0 85.3 1.0

Fluorine binding site 5 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:80.9 occ:1.00 F23 G:X3O301 0.0 80.9 1.0 C21 G:X3O301 1.4 90.7 1.0 F24 G:X3O301 2.2 87.0 1.0 F22 G:X3O301 2.2 86.9 1.0 C20 G:X3O301 2.4 90.7 1.0 S18 G:X3O301 2.9 102.4 1.0 C19 G:X3O301 2.9 88.0 1.0 CB A:ALA66 3.0 59.4 1.0 CA A:PHE63 3.6 56.7 1.0 C25 G:X3O301 3.6 82.3 1.0 C17 G:X3O301 3.8 83.5 1.0 CD1 A:PHE63 3.8 63.1 1.0 O A:LEU62 4.0 48.8 1.0 O A:PHE63 4.2 57.3 1.0 CB A:PHE63 4.3 53.8 1.0 C28 G:X3O301 4.3 80.0 1.0 N A:PHE63 4.4 55.2 1.0 CD2 G:LEU37 4.4 47.8 1.0 C A:PHE63 4.4 55.9 1.0 CG G:GLU40 4.4 74.4 1.0 CA A:ALA66 4.5 57.8 1.0 C A:LEU62 4.5 51.2 1.0 CG A:PHE63 4.5 56.0 1.0 CD1 G:LEU37 4.6 56.6 0.7 CE1 A:PHE63 4.7 63.3 1.0 C16 G:X3O301 4.8 71.3 1.0 C26 G:X3O301 4.8 84.0 1.0 NE G:ARG36 4.8 77.3 1.0 CZ G:ARG36 4.9 80.7 1.0 CD G:GLU40 4.9 80.2 1.0 OE2 G:GLU40 4.9 74.4 1.0 NH2 G:ARG36 4.9 81.6 1.0 CG G:ARG36 4.9 66.8 1.0

Fluorine binding site 6 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:87.0 occ:1.00 F24 G:X3O301 0.0 87.0 1.0 C21 G:X3O301 1.4 90.7 1.0 F22 G:X3O301 2.2 86.9 1.0 F23 G:X3O301 2.2 80.9 1.0 C20 G:X3O301 2.4 90.7 1.0 CZ G:ARG36 3.0 80.7 1.0 OE2 G:GLU40 3.0 74.4 1.0 NE G:ARG36 3.1 77.3 1.0 CG G:GLU40 3.2 74.4 1.0 NH1 G:ARG36 3.3 79.0 1.0 C25 G:X3O301 3.3 82.3 1.0 C19 G:X3O301 3.3 88.0 1.0 O G:ARG36 3.3 56.0 1.0 CD G:GLU40 3.4 80.2 1.0 NH2 G:ARG36 3.4 81.6 1.0 CG G:ARG36 3.7 66.8 1.0 CD G:ARG36 3.7 69.5 1.0 S18 G:X3O301 3.8 102.4 1.0 C G:ARG36 4.1 55.5 1.0 CD1 A:PHE63 4.3 63.1 1.0 OE1 G:GLU40 4.5 77.0 1.0 C26 G:X3O301 4.5 84.0 1.0 C28 G:X3O301 4.6 80.0 1.0 CB G:GLU40 4.6 62.9 1.0 CA G:LEU37 4.6 51.6 1.0 N G:LEU37 4.6 53.2 1.0 CB G:ARG36 4.7 61.0 1.0 CB A:ALA66 4.8 59.4 1.0 CE1 A:PHE63 4.8 63.3 1.0 CD2 G:LEU37 4.9 47.8 1.0 CA G:ARG36 4.9 60.4 1.0

Fluorine binding site 7 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:100.1 occ:1.00 F37 G:X3O301 0.0 100.1 1.0 C36 G:X3O301 1.4 95.0 1.0 F39 G:X3O301 2.2 91.4 1.0 F38 G:X3O301 2.3 95.4 1.0 C35 G:X3O301 2.3 90.1 1.0 C40 G:X3O301 2.7 89.0 1.0 C34 G:X3O301 3.6 84.8 1.0 C41 G:X3O301 4.1 83.8 1.0 N33 G:X3O301 4.7 82.1 1.0 CZ G:PHE126 4.8 48.6 1.0 C32 G:X3O301 4.9 84.2 1.0

Fluorine binding site 8 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:95.4 occ:1.00 F38 G:X3O301 0.0 95.4 1.0 C36 G:X3O301 1.4 95.0 1.0 F39 G:X3O301 2.3 91.4 1.0 F37 G:X3O301 2.3 100.1 1.0 C35 G:X3O301 2.4 90.1 1.0 C34 G:X3O301 2.8 84.8 1.0 C40 G:X3O301 3.6 89.0 1.0 CZ G:PHE126 4.1 48.6 1.0 N33 G:X3O301 4.1 82.1 1.0 CE2 G:TYR74 4.3 62.6 1.0 CE2 G:PHE126 4.4 50.4 1.0 C41 G:X3O301 4.7 83.8 1.0 OH G:TYR74 4.7 75.7 1.0 C32 G:X3O301 4.9 84.2 1.0

Fluorine binding site 9 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


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 E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ G:F301 b:91.4 occ:1.00 F39 G:X3O301 0.0 91.4 1.0 C36 G:X3O301 1.4 95.0 1.0 F37 G:X3O301 2.2 100.1 1.0 F38 G:X3O301 2.3 95.4 1.0 C35 G:X3O301 2.3 90.1 1.0 CZ G:PHE126 2.8 48.6 1.0 C34 G:X3O301 3.1 84.8 1.0 C40 G:X3O301 3.2 89.0 1.0 CE1 G:PHE126 3.3 47.0 1.0 CE2 G:PHE126 3.4 50.4 1.0 CD2 G:LEU203 4.0 53.2 1.0 CD1 G:PHE126 4.3 45.2 1.0 N33 G:X3O301 4.3 82.1 1.0 C41 G:X3O301 4.4 83.8 1.0 CD2 G:PHE126 4.4 45.7 1.0 CG G:PHE126 4.7 49.2 1.0 C32 G:X3O301 4.8 84.2 1.0

Fluorine binding site 10 out of 27 in the Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of E. Coli Clpp Protease in Complex with Phosphine Oxide Compound ACP6-12 within 5.0Å range: probe atom residue distance (Å) B Occ X:F301 b:64.8 occ:1.00 F08 X:X3O301 0.0 64.8 1.0 C07 X:X3O301 1.4 66.1 1.0 F10 X:X3O301 2.2 63.0 1.0 F09 X:X3O301 2.3 65.2 1.0 C06 X:X3O301 2.4 64.0 1.0 C11 X:X3O301 2.8 68.8 1.0 CD2 Y:LEU62 3.5 43.3 1.0 CD2 Y:PHE96 3.6 50.5 1.0 CG2 Y:THR93 3.7 33.4 1.0 CA Y:THR93 3.7 39.4 1.0 C05 X:X3O301 3.7 66.7 1.0 OG1 Y:THR93 3.9 39.9 1.0 CB Y:THR93 3.9 38.3 1.0 CB Y:PHE96 4.0 43.3 1.0 CG Y:PHE96 4.0 46.5 1.0 N12 X:X3O301 4.1 64.8 1.0 CG2 Y:ILE97 4.1 42.9 1.0 O Y:THR93 4.4 37.0 1.0 CE2 Y:PHE96 4.5 55.8 1.0 CG Y:LEU62 4.5 50.6 1.0 N Y:THR93 4.6 39.1 1.0 C Y:THR93 4.6 37.9 1.0 CD1 Y:LEU62 4.7 48.9 1.0 OH X:TYR76 4.7 46.3 1.0 CE2 X:TYR76 4.8 48.0 1.0 C04 X:X3O301 4.8 66.5 1.0 C03 X:X3O301 4.9 68.5 1.0

F.Lin, M.F.Mabanglo, J.L.Zhou, G.Binepal, M.M.Barghash, K.S.Wong, S.D.Gray-Owen, R.A.Batey, W.A.Houry. Structure-Based Design and Development of Phosphine Oxides As A Novel Chemotype For Antibiotics That Dysregulate Bacterial Clpp Proteases. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 39221504
DOI: 10.1021/ACS.JMEDCHEM.4C00773