Fluorine in PDB 4ddy: Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10

All present enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10:
3.5.2.6;

The structure of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10, PDB code: 4ddy was solved by D.A.Nichols, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.014, 107.105, 47.509, 90.00, 102.11, 90.00
R / Rfree (%)	17.1 / 20.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Fluorine atom in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 (pdb code 4ddy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 36 binding sites of Fluorine where determined in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10, PDB code: 4ddy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:14.5 occ:1.00 F24 A:DN6301 0.0 14.5 1.0 C7 A:DN6301 1.4 12.4 1.0 F23 A:DN6301 2.2 13.5 1.0 F22 A:DN6301 2.3 15.1 1.0 C6 A:DN6301 2.3 11.8 1.0 C5 A:DN6301 3.1 11.2 1.0 O A:PRO167 3.1 10.0 1.0 N A:THR171 3.2 10.0 1.0 C1 A:DN6301 3.2 11.7 1.0 C A:ASN170 3.3 9.6 1.0 CG2 A:THR171 3.4 11.2 1.0 CA A:THR171 3.5 10.2 1.0 CA A:THR168 3.7 9.9 1.0 O A:ASN170 3.8 10.4 1.0 O A:THR168 3.8 10.4 1.0 CA A:ASN170 3.9 9.5 1.0 N A:ASN170 3.9 9.3 1.0 CB A:ASN170 3.9 9.6 1.0 C A:THR168 3.9 9.5 1.0 C A:PRO167 4.0 9.7 1.0 CB A:THR171 4.1 10.3 1.0 N A:THR168 4.3 9.8 1.0 C4 A:DN6301 4.3 10.6 1.0 C2 A:DN6301 4.4 11.7 1.0 CB A:THR168 4.7 10.3 1.0 N A:LEU169 4.8 9.7 1.0 C3 A:DN6301 4.9 11.5 1.0 OD2 A:ASP240 4.9 14.4 1.0 C A:THR171 4.9 10.4 1.0 OG1 A:THR171 4.9 10.7 1.0 CB A:PRO167 5.0 10.2 1.0 ND2 A:ASN170 5.0 10.2 1.0

Fluorine binding site 2 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:15.1 occ:1.00 F22 A:DN6301 0.0 15.1 1.0 C7 A:DN6301 1.3 12.4 1.0 F23 A:DN6301 2.1 13.5 1.0 F24 A:DN6301 2.3 14.5 1.0 C6 A:DN6301 2.3 11.8 1.0 C1 A:DN6301 2.7 11.7 1.0 O A:HOH539 3.1 32.6 1.0 C5 A:DN6301 3.6 11.2 1.0 OD2 A:ASP240 3.8 14.4 1.0 C2 A:DN6301 4.1 11.7 1.0 CG2 A:THR171 4.1 11.2 1.0 CG A:ASP240 4.6 12.0 1.0 CA A:THR171 4.7 10.2 1.0 C4 A:DN6301 4.8 10.6 1.0 O A:PRO167 4.9 10.0 1.0 OD1 A:ASP240 4.9 13.6 1.0 C3 A:DN6301 4.9 11.5 1.0 N A:THR171 5.0 10.0 1.0

Fluorine binding site 3 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:13.5 occ:1.00 F23 A:DN6301 0.0 13.5 1.0 C7 A:DN6301 1.3 12.4 1.0 F22 A:DN6301 2.1 15.1 1.0 F24 A:DN6301 2.2 14.5 1.0 C6 A:DN6301 2.3 11.8 1.0 C5 A:DN6301 2.8 11.2 1.0 O A:PRO167 3.3 10.0 1.0 C1 A:DN6301 3.5 11.7 1.0 CB A:PRO167 3.6 10.2 1.0 C A:PRO167 3.7 9.7 1.0 CG A:PRO167 3.8 10.8 1.0 CA A:THR168 4.0 9.9 1.0 N A:THR168 4.1 9.8 1.0 C4 A:DN6301 4.2 10.6 1.0 CA A:PRO167 4.3 9.9 1.0 C2 A:DN6301 4.7 11.7 1.0 CG2 A:THR168 4.7 11.4 1.0 ND2 A:ASN104 4.8 12.3 1.0 CG2 A:THR171 4.9 11.2 1.0 CB A:THR168 4.9 10.3 1.0 C3 A:DN6301 4.9 11.5 1.0 C A:THR168 4.9 9.5 1.0 O21 A:DN6301 5.0 11.3 1.0

Fluorine binding site 4 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:19.3 occ:1.00 F24 A:DN6302 0.0 19.3 1.0 C7 A:DN6302 1.3 17.1 1.0 F22 A:DN6302 2.1 18.0 1.0 F23 A:DN6302 2.2 19.3 1.0 C6 A:DN6302 2.4 16.0 1.0 C1 A:DN6302 2.7 15.5 1.0 CG2 A:THR216 3.2 9.8 1.0 N18 A:DN6301 3.2 11.3 1.0 CB A:THR216 3.3 9.5 1.0 N17 A:DN6301 3.3 10.8 1.0 O A:HOH413 3.6 13.8 1.0 C5 A:DN6302 3.6 14.9 1.0 OG1 A:THR216 3.9 10.1 1.0 OG1 A:THR235 3.9 9.7 1.0 N19 A:DN6301 4.0 11.5 1.0 C2 A:DN6302 4.1 14.7 1.0 C16 A:DN6301 4.1 9.8 1.0 CB A:SER130 4.4 9.3 1.0 N20 A:DN6301 4.4 10.7 1.0 CA A:THR216 4.5 9.3 1.0 C4 A:DN6302 4.7 14.9 1.0 O A:THR216 4.8 10.2 1.0 O A:HOH412 4.8 12.2 1.0 OH A:TYR105 4.8 15.5 1.0 OG A:SER130 4.8 10.6 1.0 C3 A:DN6302 4.9 14.6 1.0

Fluorine binding site 5 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:18.0 occ:1.00 F22 A:DN6302 0.0 18.0 1.0 C7 A:DN6302 1.3 17.1 1.0 F24 A:DN6302 2.1 19.3 1.0 F23 A:DN6302 2.1 19.3 1.0 C6 A:DN6302 2.3 16.0 1.0 C5 A:DN6302 2.8 14.9 1.0 CE1 A:TYR105 3.1 11.8 1.0 OH A:TYR105 3.2 15.5 1.0 CZ A:TYR105 3.4 12.6 1.0 N17 A:DN6301 3.4 10.8 1.0 CB A:SER130 3.5 9.3 1.0 C1 A:DN6302 3.5 15.5 1.0 O A:TYR129 3.7 10.7 1.0 O A:HOH418 3.9 13.4 1.0 C13 A:DN6301 3.9 10.1 1.0 C16 A:DN6301 4.0 9.8 1.0 CG2 A:THR216 4.0 9.8 1.0 N18 A:DN6301 4.1 11.3 1.0 C4 A:DN6302 4.1 14.9 1.0 CD1 A:TYR105 4.1 11.0 1.0 OG A:SER130 4.2 10.6 1.0 C12 A:DN6301 4.3 9.6 1.0 CE2 A:TYR105 4.5 11.7 1.0 C A:TYR129 4.6 9.7 1.0 C2 A:DN6302 4.6 14.7 1.0 CA A:SER130 4.7 9.6 1.0 O A:SER130 4.7 10.3 1.0 N20 A:DN6301 4.8 10.7 1.0 CB A:THR216 4.8 9.5 1.0 C3 A:DN6302 4.8 14.6 1.0 C14 A:DN6301 4.9 10.5 1.0 N19 A:DN6301 4.9 11.5 1.0

Fluorine binding site 6 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:19.3 occ:1.00 F23 A:DN6302 0.0 19.3 1.0 C7 A:DN6302 1.3 17.1 1.0 F22 A:DN6302 2.1 18.0 1.0 F24 A:DN6302 2.2 19.3 1.0 C6 A:DN6302 2.3 16.0 1.0 OH A:TYR105 3.0 15.5 1.0 C5 A:DN6302 3.1 14.9 1.0 C1 A:DN6302 3.1 15.5 1.0 CZ A:TYR105 3.9 12.6 1.0 O A:HOH418 3.9 13.4 1.0 CG2 A:THR216 4.0 9.8 1.0 C4 A:DN6302 4.3 14.9 1.0 CE1 A:TYR105 4.3 11.8 1.0 C2 A:DN6302 4.3 14.7 1.0 CB A:THR216 4.6 9.5 1.0 O A:HOH413 4.8 13.8 1.0 C3 A:DN6302 4.8 14.6 1.0 CE2 A:TYR105 4.8 11.7 1.0 O A:HOH523 4.9 38.9 1.0 N17 A:DN6301 5.0 10.8 1.0

Fluorine binding site 7 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:22.0 occ:1.00 F24 A:DN6303 0.0 22.0 1.0 C7 A:DN6303 1.3 19.4 1.0 F23 A:DN6303 2.1 21.1 1.0 F22 A:DN6303 2.1 22.3 1.0 C6 A:DN6303 2.3 19.4 1.0 O A:HOH558 3.1 26.3 1.0 N19 A:DN6304 3.1 19.0 1.0 C1 A:DN6303 3.2 19.6 1.0 C5 A:DN6303 3.2 18.4 1.0 CA A:GLY196 3.3 13.6 1.0 OE1 A:GLN192 3.3 19.4 1.0 CD A:GLN192 3.4 15.9 1.0 N20 A:DN6304 3.5 18.9 1.0 NE2 A:GLN192 3.5 17.6 1.0 N18 A:DN6304 3.6 19.2 1.0 C16 A:DN6304 4.1 17.9 1.0 N17 A:DN6304 4.1 16.8 1.0 N A:GLY196 4.1 13.5 1.0 N A:HIS197 4.2 14.2 1.0 C A:GLY196 4.3 13.7 1.0 CA A:GLN192 4.3 10.9 1.0 CG A:GLN192 4.4 13.1 1.0 C2 A:DN6303 4.4 19.4 1.0 C4 A:DN6303 4.4 18.6 1.0 O A:HOH584 4.5 25.3 1.0 O A:HOH624 4.5 37.4 1.0 CB A:GLN192 4.8 11.2 1.0 O A:ARG191 4.9 10.8 1.0 C3 A:DN6303 4.9 18.2 1.0 N A:GLN192 4.9 10.4 1.0 C A:LEU195 5.0 13.1 1.0

Fluorine binding site 8 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:22.3 occ:1.00 F22 A:DN6303 0.0 22.3 1.0 C7 A:DN6303 1.3 19.4 1.0 F24 A:DN6303 2.1 22.0 1.0 F23 A:DN6303 2.2 21.1 1.0 C6 A:DN6303 2.3 19.4 1.0 C5 A:DN6303 2.7 18.4 1.0 O A:HOH584 3.2 25.3 1.0 CA A:GLY196 3.3 13.6 1.0 NE A:ARG191 3.3 15.9 1.0 O A:HOH489 3.4 22.0 1.0 N A:GLY196 3.4 13.5 1.0 C1 A:DN6303 3.6 19.6 1.0 CG A:ARG191 3.7 12.1 1.0 CD A:ARG191 3.8 14.1 1.0 C A:LEU195 3.8 13.1 1.0 O A:ARG191 3.9 10.8 1.0 O A:LEU195 4.0 14.5 1.0 C4 A:DN6303 4.1 18.6 1.0 CZ A:ARG191 4.2 16.1 1.0 C A:ARG191 4.3 10.4 1.0 CB A:LEU195 4.4 13.0 1.0 NH2 A:ARG191 4.5 17.9 1.0 O A:HOH624 4.5 37.4 1.0 CA A:GLN192 4.6 10.9 1.0 N A:GLN192 4.7 10.4 1.0 C2 A:DN6303 4.7 19.4 1.0 CA A:LEU195 4.7 12.7 1.0 N18 A:DN6304 4.7 19.2 1.0 C A:GLY196 4.7 13.7 1.0 N19 A:DN6304 4.8 19.0 1.0 CB A:ARG191 4.8 10.8 1.0 C3 A:DN6303 4.9 18.2 1.0 CD A:GLN192 5.0 15.9 1.0 O A:HOH558 5.0 26.3 1.0 OE1 A:GLN192 5.0 19.4 1.0 N17 A:DN6304 5.0 16.8 1.0

Fluorine binding site 9 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:21.1 occ:1.00 F23 A:DN6303 0.0 21.1 1.0 C7 A:DN6303 1.3 19.4 1.0 F24 A:DN6303 2.1 22.0 1.0 F22 A:DN6303 2.2 22.3 1.0 C6 A:DN6303 2.4 19.4 1.0 C1 A:DN6303 2.8 19.6 1.0 CD A:GLN192 3.3 15.9 1.0 CD A:ARG191 3.4 14.1 1.0 NE2 A:GLN192 3.4 17.6 1.0 CG A:GLN192 3.5 13.1 1.0 CA A:GLN192 3.5 10.9 1.0 N A:GLN192 3.5 10.4 1.0 CG A:ARG191 3.5 12.1 1.0 C5 A:DN6303 3.6 18.4 1.0 C A:ARG191 3.7 10.4 1.0 NE A:ARG191 3.7 15.9 1.0 OE1 A:GLN192 3.8 19.4 1.0 O A:ARG191 3.9 10.8 1.0 CB A:GLN192 4.0 11.2 1.0 CB A:ARG191 4.0 10.8 1.0 C2 A:DN6303 4.2 19.4 1.0 CA A:GLY196 4.3 13.6 1.0 OE1 A:GLN188 4.3 13.0 0.4 CA A:ARG191 4.5 10.5 1.0 N A:GLY196 4.5 13.5 1.0 CZ A:ARG191 4.6 16.1 1.0 O A:GLN188 4.7 10.5 0.5 O A:GLN188 4.7 9.9 0.5 C4 A:DN6303 4.7 18.6 1.0 O A:HOH558 4.8 26.3 1.0 C A:GLN192 4.8 10.4 1.0 C3 A:DN6303 5.0 18.2 1.0

Fluorine binding site 10 out of 36 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:27.8 occ:1.00 F24 A:DN6304 0.0 27.8 1.0 C7 A:DN6304 1.3 25.9 1.0 F23 A:DN6304 2.1 27.2 1.0 F22 A:DN6304 2.2 27.7 1.0 C6 A:DN6304 2.3 24.2 1.0 C1 A:DN6304 2.7 24.3 1.0 C5 A:DN6304 3.5 23.5 1.0 C2 A:DN6304 4.1 23.4 1.0 C4 A:DN6304 4.6 22.6 1.0 C3 A:DN6304 4.9 22.8 1.0

D.A.Nichols, P.Jaishankar, W.Larson, E.Smith, G.Liu, R.Beyrouthy, R.Bonnet, A.R.Renslo, Y.Chen. Structure-Based Design of Potent and Ligand-Efficient Inhibitors of Ctx-M Class A Beta-Lactamase J.Med.Chem. V. 55 2163 2012.
ISSN: ISSN 0022-2623
PubMed: 22296601
DOI: 10.1021/JM2014138