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Iron in PDB 6nlm: 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)

Enzymatic activity of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)

All present enzymatic activity of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15):
1.16.3.1;

Protein crystallography data

The structure of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15), PDB code: 6nlm was solved by S.Lovell, A.Punchi-Hewage, K.P.Battaile, H.Yao, B.Nammalwar, K.K.Gnanasekaran, R.A.Bunce, A.B.Reitz, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.93 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 130.247, 194.970, 203.030, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.4

Iron Binding Sites:

The binding sites of Iron atom in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) (pdb code 6nlm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15), PDB code: 6nlm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6nlm

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Iron binding site 1 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:13.8
occ:1.00
OD1 E:ASN148 2.8 15.1 1.0
OD1 K:ASN148 2.8 14.0 1.0
OD1 J:ASN148 2.8 12.9 1.0
OD1 A:ASN148 2.8 13.6 1.0
OE1 E:GLN151 2.9 13.1 1.0
OE1 K:GLN151 2.9 15.0 1.0
OE1 J:GLN151 3.0 15.3 1.0
OE1 A:GLN151 3.0 17.1 1.0
CG E:ASN148 3.6 13.5 1.0
CG K:ASN148 3.6 17.4 1.0
CG J:ASN148 3.7 16.1 1.0
CG A:ASN148 3.7 16.9 1.0
CD K:GLN151 3.9 18.3 1.0
CD E:GLN151 3.9 13.9 1.0
CD A:GLN151 3.9 13.5 1.0
CD J:GLN151 3.9 15.7 1.0
ND2 K:ASN148 4.0 20.4 1.0
ND2 E:ASN148 4.0 16.5 1.0
ND2 J:ASN148 4.0 14.3 1.0
NE2 K:GLN151 4.1 15.6 1.0
ND2 A:ASN148 4.1 15.1 1.0
NE2 E:GLN151 4.1 13.5 1.0
NE2 A:GLN151 4.1 16.4 1.0
NE2 J:GLN151 4.2 15.4 1.0
CB E:ASN148 4.8 12.5 1.0
CB A:ASN148 4.9 10.6 1.0
CB K:ASN148 4.9 13.7 1.0
CB J:ASN148 4.9 13.8 1.0

Iron binding site 2 out of 10 in 6nlm

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Iron binding site 2 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:17.9
occ:1.00
FE A:HEM203 0.0 17.9 1.0
NB A:HEM203 2.0 13.3 1.0
NC A:HEM203 2.0 14.6 1.0
NA A:HEM203 2.1 14.9 1.0
ND A:HEM203 2.1 17.7 1.0
SD A:MET52 2.4 14.9 1.0
C4B A:HEM203 3.0 12.8 1.0
C1B A:HEM203 3.0 14.4 1.0
C4C A:HEM203 3.0 16.5 1.0
C1C A:HEM203 3.0 16.8 1.0
C4A A:HEM203 3.1 16.6 1.0
C4D A:HEM203 3.1 11.7 1.0
C1A A:HEM203 3.1 15.8 1.0
C1D A:HEM203 3.1 16.2 1.0
CE A:MET52 3.3 15.7 1.0
CHB A:HEM203 3.4 17.3 1.0
CHC A:HEM203 3.4 18.2 1.0
CHD A:HEM203 3.4 18.6 1.0
CHA A:HEM203 3.5 16.6 1.0
CG A:MET52 3.5 14.2 1.0
CB A:MET52 4.2 15.7 1.0
C3B A:HEM203 4.2 16.1 1.0
C2B A:HEM203 4.2 16.2 1.0
C3C A:HEM203 4.2 15.2 1.0
C2C A:HEM203 4.3 15.7 1.0
C3A A:HEM203 4.3 16.4 1.0
C2A A:HEM203 4.3 17.8 1.0
C3D A:HEM203 4.3 17.2 1.0
C2D A:HEM203 4.3 22.6 1.0

Iron binding site 3 out of 10 in 6nlm

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Iron binding site 3 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:13.8
occ:1.00
OD1 C:ASN148 2.8 15.2 1.0
OD1 B:ASN148 2.8 14.2 1.0
OD1 L:ASN148 2.8 14.6 1.0
OD1 G:ASN148 2.8 13.8 1.0
OE1 G:GLN151 2.9 11.7 1.0
OE1 L:GLN151 2.9 13.6 1.0
OE1 C:GLN151 2.9 14.0 1.0
OE1 B:GLN151 2.9 14.8 1.0
CG L:ASN148 3.7 15.0 1.0
CG C:ASN148 3.7 16.6 1.0
CG G:ASN148 3.7 13.2 1.0
CG B:ASN148 3.7 17.6 1.0
CD G:GLN151 3.8 13.6 1.0
CD L:GLN151 3.9 12.7 1.0
CD B:GLN151 3.9 14.2 1.0
CD C:GLN151 3.9 17.6 1.0
ND2 G:ASN148 4.0 20.4 1.0
ND2 L:ASN148 4.0 16.5 1.0
NE2 G:GLN151 4.1 16.1 1.0
ND2 B:ASN148 4.1 17.3 1.0
ND2 C:ASN148 4.1 15.2 1.0
NE2 B:GLN151 4.2 13.9 1.0
NE2 C:GLN151 4.2 14.9 1.0
NE2 L:GLN151 4.2 15.5 1.0
CB C:ASN148 4.8 11.4 1.0
CB G:ASN148 4.9 13.9 1.0
CB B:ASN148 4.9 13.3 1.0
CB L:ASN148 4.9 15.7 1.0

Iron binding site 4 out of 10 in 6nlm

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Iron binding site 4 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:16.5
occ:1.00
FE B:HEM203 0.0 16.5 1.0
NC B:HEM203 2.0 15.3 1.0
ND B:HEM203 2.0 16.3 1.0
NB B:HEM203 2.0 14.7 1.0
NA B:HEM203 2.1 15.9 1.0
SD E:MET52 2.3 14.0 1.0
SD B:MET52 2.3 14.5 1.0
C4C B:HEM203 3.0 15.7 1.0
C1C B:HEM203 3.0 16.3 1.0
C4B B:HEM203 3.0 13.9 1.0
C1D B:HEM203 3.0 13.4 1.0
C4D B:HEM203 3.1 13.4 1.0
C1B B:HEM203 3.1 13.6 1.0
C1A B:HEM203 3.1 16.6 1.0
C4A B:HEM203 3.1 16.8 1.0
CE B:MET52 3.3 21.4 1.0
CE E:MET52 3.3 14.8 1.0
CHC B:HEM203 3.4 15.9 1.0
CHD B:HEM203 3.4 15.6 1.0
CHB B:HEM203 3.5 14.4 1.0
CHA B:HEM203 3.5 15.5 1.0
CG E:MET52 3.5 13.3 1.0
CG B:MET52 3.5 19.1 1.0
C3C B:HEM203 4.2 16.9 1.0
CB B:MET52 4.2 13.0 1.0
CB E:MET52 4.2 16.4 1.0
C2C B:HEM203 4.3 16.3 1.0
C3B B:HEM203 4.3 14.2 1.0
C2D B:HEM203 4.3 18.4 1.0
C3D B:HEM203 4.3 17.9 1.0
C2B B:HEM203 4.3 16.9 1.0
C2A B:HEM203 4.3 17.3 1.0
C3A B:HEM203 4.3 18.9 1.0

Iron binding site 5 out of 10 in 6nlm

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Iron binding site 5 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:17.9
occ:1.00
FE C:HEM202 0.0 17.9 1.0
ND C:HEM202 2.0 19.3 1.0
NC C:HEM202 2.0 17.2 1.0
NA C:HEM202 2.0 17.3 1.0
NB C:HEM202 2.1 17.6 1.0
SD C:MET52 2.3 13.6 1.0
SD I:MET52 2.4 15.1 1.0
C4D C:HEM202 3.0 16.0 1.0
C1A C:HEM202 3.0 21.0 1.0
C4C C:HEM202 3.0 16.0 1.0
C1C C:HEM202 3.0 17.7 1.0
C1D C:HEM202 3.0 18.9 1.0
C4B C:HEM202 3.0 14.9 1.0
C4A C:HEM202 3.1 18.4 1.0
C1B C:HEM202 3.1 15.7 1.0
CE I:MET52 3.3 17.7 1.0
CE C:MET52 3.4 13.3 1.0
CHA C:HEM202 3.4 19.4 1.0
CHC C:HEM202 3.4 14.4 1.0
CHD C:HEM202 3.4 16.8 1.0
CG C:MET52 3.4 12.6 1.0
CHB C:HEM202 3.5 18.1 1.0
CG I:MET52 3.5 14.1 1.0
CB C:MET52 4.2 13.5 1.0
CB I:MET52 4.2 13.5 1.0
C3D C:HEM202 4.2 19.5 1.0
C2D C:HEM202 4.2 20.1 1.0
C3C C:HEM202 4.2 14.9 1.0
C2C C:HEM202 4.3 19.6 1.0
C2A C:HEM202 4.3 17.0 1.0
C3B C:HEM202 4.3 16.5 1.0
C3A C:HEM202 4.3 15.9 1.0
C2B C:HEM202 4.3 16.2 1.0

Iron binding site 6 out of 10 in 6nlm

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Iron binding site 6 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:14.2
occ:1.00
OD1 D:ASN148 2.8 14.6 1.0
OD1 F:ASN148 2.8 13.9 1.0
OD1 I:ASN148 2.9 15.1 1.0
OE1 I:GLN151 2.9 17.3 1.0
OE1 F:GLN151 2.9 15.4 1.0
OE1 D:GLN151 3.0 12.4 1.0
CG F:ASN148 3.7 15.4 1.0
CG D:ASN148 3.7 18.9 1.0
CG I:ASN148 3.7 14.0 1.0
CD F:GLN151 3.9 14.6 1.0
CD I:GLN151 3.9 13.7 1.0
CD D:GLN151 3.9 18.0 1.0
ND2 I:ASN148 4.0 18.2 1.0
ND2 F:ASN148 4.0 16.1 1.0
ND2 D:ASN148 4.1 18.6 1.0
NE2 F:GLN151 4.1 16.1 1.0
NE2 D:GLN151 4.2 15.2 1.0
NE2 I:GLN151 4.2 15.8 1.0
CB D:ASN148 4.9 16.3 1.0
CB F:ASN148 4.9 12.1 1.0
CB I:ASN148 5.0 12.8 1.0

Iron binding site 7 out of 10 in 6nlm

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Iron binding site 7 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe203

b:17.5
occ:0.50
FE D:HEM203 0.0 17.5 0.5
NC D:HEM203 2.0 14.7 0.5
NB D:HEM203 2.0 14.2 0.5
ND D:HEM203 2.1 15.0 0.5
NA D:HEM203 2.1 15.1 0.5
SD D:MET52 2.4 15.2 1.0
C4C D:HEM203 3.0 14.2 0.5
C1C D:HEM203 3.0 14.6 0.5
C4B D:HEM203 3.1 15.1 0.5
C1D D:HEM203 3.1 15.7 0.5
C1B D:HEM203 3.1 14.0 0.5
C4A D:HEM203 3.1 15.9 0.5
C4D D:HEM203 3.1 17.0 0.5
C1A D:HEM203 3.1 17.0 0.5
CE D:MET52 3.3 15.7 1.0
CHD D:HEM203 3.4 13.8 0.5
CHC D:HEM203 3.4 12.9 0.5
CHB D:HEM203 3.5 14.6 0.5
CHA D:HEM203 3.5 16.7 0.5
CG D:MET52 3.5 12.6 1.0
C3C D:HEM203 4.2 13.9 0.5
C2C D:HEM203 4.2 11.9 0.5
C3B D:HEM203 4.3 13.5 0.5
C2D D:HEM203 4.3 15.9 0.5
C2B D:HEM203 4.3 11.7 0.5
C2A D:HEM203 4.3 17.0 0.5
CB D:MET52 4.3 13.7 1.0
C3D D:HEM203 4.3 17.0 0.5
C3A D:HEM203 4.3 16.4 0.5

Iron binding site 8 out of 10 in 6nlm

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Iron binding site 8 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:17.1
occ:1.00
FE F:HEM202 0.0 17.1 1.0
NB F:HEM202 2.0 14.4 1.0
ND F:HEM202 2.0 16.6 1.0
NC F:HEM202 2.0 13.2 1.0
NA F:HEM202 2.1 18.4 1.0
SD F:MET52 2.4 14.8 1.0
SD K:MET52 2.4 14.7 1.0
C4B F:HEM202 3.0 13.4 1.0
C4D F:HEM202 3.0 19.6 1.0
C4C F:HEM202 3.0 18.1 1.0
C1D F:HEM202 3.1 16.7 1.0
C1A F:HEM202 3.1 16.9 1.0
C1C F:HEM202 3.1 12.9 1.0
C1B F:HEM202 3.1 15.7 1.0
C4A F:HEM202 3.1 15.7 1.0
CE F:MET52 3.3 15.4 1.0
CE K:MET52 3.3 13.5 1.0
CHA F:HEM202 3.4 16.9 1.0
CHD F:HEM202 3.4 17.7 1.0
CHC F:HEM202 3.4 16.1 1.0
CG F:MET52 3.4 13.6 1.0
CG K:MET52 3.5 12.7 1.0
CHB F:HEM202 3.5 15.7 1.0
CB F:MET52 4.2 14.8 1.0
CB K:MET52 4.2 13.1 1.0
C3B F:HEM202 4.2 14.5 1.0
C3D F:HEM202 4.2 18.6 1.0
C3C F:HEM202 4.3 17.4 1.0
C2D F:HEM202 4.3 20.0 1.0
C2C F:HEM202 4.3 15.9 1.0
C2B F:HEM202 4.3 16.4 1.0
C2A F:HEM202 4.3 21.1 1.0
C3A F:HEM202 4.3 20.7 1.0
CD1 K:ILE49 5.0 28.3 1.0

Iron binding site 9 out of 10 in 6nlm

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Iron binding site 9 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe202

b:16.6
occ:1.00
FE H:HEM202 0.0 16.6 1.0
ND H:HEM202 2.0 19.0 1.0
NB H:HEM202 2.0 18.8 1.0
NA H:HEM202 2.0 14.0 1.0
NC H:HEM202 2.1 16.3 1.0
SD H:MET52 2.3 15.3 1.0
SD J:MET52 2.4 14.2 1.0
C1A H:HEM202 3.0 14.0 1.0
C1D H:HEM202 3.0 19.9 1.0
C4D H:HEM202 3.0 21.8 1.0
C4B H:HEM202 3.0 16.6 1.0
C4C H:HEM202 3.1 15.8 1.0
C1B H:HEM202 3.1 13.8 1.0
C1C H:HEM202 3.1 14.9 1.0
C4A H:HEM202 3.1 16.4 1.0
CE J:MET52 3.3 16.6 1.0
CE H:MET52 3.3 15.6 1.0
CHA H:HEM202 3.4 13.2 1.0
CHD H:HEM202 3.4 12.8 1.0
CHC H:HEM202 3.4 17.5 1.0
CG H:MET52 3.5 14.0 1.0
CHB H:HEM202 3.5 13.5 1.0
CG J:MET52 3.5 14.0 1.0
CB H:MET52 4.2 15.1 1.0
C2D H:HEM202 4.2 18.7 1.0
CB J:MET52 4.2 12.4 1.0
C3D H:HEM202 4.2 19.4 1.0
C2A H:HEM202 4.3 13.9 1.0
C3B H:HEM202 4.3 15.9 1.0
C2B H:HEM202 4.3 14.9 1.0
C3A H:HEM202 4.3 19.5 1.0
C3C H:HEM202 4.3 13.6 1.0
C2C H:HEM202 4.3 15.2 1.0

Iron binding site 10 out of 10 in 6nlm

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Iron binding site 10 out of 10 in the 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 1.90 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor (Analog 15) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe202

b:16.9
occ:0.50
FE L:HEM202 0.0 16.9 0.5
NA L:HEM202 2.0 16.8 0.5
ND L:HEM202 2.0 17.2 0.5
NC L:HEM202 2.1 16.4 0.5
NB L:HEM202 2.1 15.7 0.5
SD L:MET52 2.4 14.8 1.0
C1A L:HEM202 3.0 19.2 0.5
C4A L:HEM202 3.0 16.2 0.5
C4D L:HEM202 3.1 18.7 0.5
C4C L:HEM202 3.1 17.2 0.5
C1D L:HEM202 3.1 16.0 0.5
C1B L:HEM202 3.1 17.6 0.5
C1C L:HEM202 3.1 15.9 0.5
C4B L:HEM202 3.1 16.5 0.5
CE L:MET52 3.3 13.6 1.0
CHD L:HEM202 3.4 17.6 0.5
CHA L:HEM202 3.4 16.9 0.5
CHB L:HEM202 3.4 17.2 0.5
CHC L:HEM202 3.5 16.7 0.5
CG L:MET52 3.6 13.8 1.0
C2A L:HEM202 4.2 17.7 0.5
C3A L:HEM202 4.2 16.9 0.5
C3D L:HEM202 4.3 18.3 0.5
C2D L:HEM202 4.3 17.1 0.5
C3C L:HEM202 4.3 12.9 0.5
C2B L:HEM202 4.3 14.3 0.5
C2C L:HEM202 4.3 15.3 0.5
C3B L:HEM202 4.3 13.3 0.5
CB L:MET52 4.3 12.8 1.0

Reference:

A.N.D.Punchi Hewage, H.Yao, B.Nammalwar, K.K.Gnanasekaran, S.Lovell, R.A.Bunce, K.Eshelman, S.M.Phaniraj, M.M.Lee, B.R.Peterson, K.P.Battaile, A.B.Reitz, M.Rivera. Small Molecule Inhibitors of the Bfrb-Bfd Interaction Decrease Pseudomonas Aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J.Am.Chem.Soc. V. 141 8171 2019.
ISSN: ESSN 1520-5126
PubMed: 31038945
DOI: 10.1021/JACS.9B00394
Page generated: Wed Aug 7 03:45:55 2024

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