Atomistry » Fluorine » PDB 4dbu-4e28 » 4ddy
Atomistry »
  Fluorine »
    PDB 4dbu-4e28 »
      4ddy »

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

Enzymatic activity of 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;

Protein crystallography data

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

Fluorine Binding Sites:

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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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 4ddy

Go back to Fluorine Binding Sites List in 4ddy
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

Reference:

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
Page generated: Thu Aug 1 01:00:17 2024

Last articles

Cl in 4HG7
Cl in 4HFC
Cl in 4HFD
Cl in 4HFB
Cl in 4HE9
Cl in 4HE2
Cl in 4HEO
Cl in 4HE1
Cl in 4HBM
Cl in 4HDP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy