Atomistry » Fluorine » PDB 5sry-5tbm » 5sym
Atomistry »
  Fluorine »
    PDB 5sry-5tbm »
      5sym »

Fluorine in PDB 5sym: Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348

Protein crystallography data

The structure of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348, PDB code: 5sym was solved by J.A.Stuckey, K.J.Labby, J.L.Meagher, S.J.Won, B.R.Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.51 / 1.55
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.670, 73.690, 81.820, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.9

Other elements in 5sym:

The structure of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 (pdb code 5sym). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348, PDB code: 5sym:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 1 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:28.6
occ:1.00
F A:71Q301 0.0 28.6 1.0
C4 A:71Q301 1.3 30.0 1.0
F2 A:71Q301 2.1 33.1 1.0
F1 A:71Q301 2.1 27.7 1.0
C3 A:71Q301 2.4 27.7 1.0
H2 A:71Q301 2.6 26.9 1.0
HG13 A:ILE75 2.6 15.2 1.0
C5 A:71Q301 2.9 26.3 1.0
HE21 A:GLN120 2.9 16.1 0.5
HH2 A:TRP145 3.1 15.5 1.0
CL A:CL308 3.1 14.1 1.0
HD12 A:ILE75 3.2 20.5 1.0
HB3 A:GLN120 3.2 13.1 0.5
HB3 A:GLN120 3.2 14.2 0.5
HG21 A:ILE75 3.2 14.9 1.0
HD11 A:ILE75 3.3 19.3 1.0
CG1 A:ILE75 3.5 14.2 1.0
CD1 A:ILE75 3.5 19.7 1.0
C2 A:71Q301 3.5 27.8 1.0
HB2 A:LEU30 3.6 16.2 1.0
HD22 A:LEU30 3.8 27.6 1.0
H1 A:71Q301 3.9 28.2 1.0
HG A:SER119 3.9 13.3 1.0
HD13 A:LEU30 3.9 23.1 1.0
NE2 A:GLN120 3.9 16.1 0.5
CH2 A:TRP145 4.1 13.1 1.0
CG2 A:ILE75 4.1 14.5 1.0
C6 A:71Q301 4.2 25.7 1.0
HG12 A:ILE75 4.2 14.4 1.0
CB A:GLN120 4.2 12.7 0.5
CB A:GLN120 4.2 11.5 0.5
HG23 A:ILE75 4.2 15.9 1.0
HG2 A:GLN120 4.3 24.5 0.5
H A:GLN120 4.3 8.2 0.5
H A:GLN120 4.3 8.2 0.5
HE21 A:GLN120 4.3 16.5 0.5
CB A:ILE75 4.4 13.5 1.0
HG2 A:GLN120 4.4 13.1 0.5
HE22 A:GLN120 4.4 16.2 0.5
HZ3 A:TRP145 4.5 13.3 1.0
CB A:LEU30 4.5 15.1 1.0
HD13 A:ILE75 4.6 19.9 1.0
HB3 A:LEU30 4.6 15.3 1.0
C1 A:71Q301 4.7 28.3 1.0
CG A:GLN120 4.7 23.9 0.5
CG A:GLN120 4.7 12.5 0.5
CZ3 A:TRP145 4.7 12.4 1.0
HB A:ILE75 4.8 12.9 1.0
CD2 A:LEU30 4.8 27.4 1.0
HB2 A:GLN120 4.8 11.9 0.5
HB2 A:GLN120 4.8 13.3 0.5
CD A:GLN120 4.8 14.6 0.5
H A:LEU30 4.8 13.8 1.0
HZ2 A:TRP145 4.8 13.0 1.0
OG A:SER119 4.8 12.6 1.0
O2 A:71Q301 4.9 21.6 1.0
NE2 A:GLN120 4.9 15.4 0.5
CD1 A:LEU30 4.9 24.1 1.0
HD22 A:LEU63 4.9 21.1 1.0
CZ2 A:TRP145 4.9 12.2 1.0
N A:GLN120 4.9 9.2 1.0
C A:71Q301 5.0 27.9 1.0
CG A:LEU30 5.0 22.8 1.0
HG22 A:ILE75 5.0 13.4 1.0

Fluorine binding site 2 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 2 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:27.7
occ:1.00
F1 A:71Q301 0.0 27.7 1.0
C4 A:71Q301 1.3 30.0 1.0
F2 A:71Q301 2.1 33.1 1.0
F A:71Q301 2.1 28.6 1.0
HG21 A:ILE75 2.3 14.9 1.0
C3 A:71Q301 2.4 27.7 1.0
HG13 A:ILE75 2.9 15.2 1.0
HD22 A:LEU63 3.0 21.1 1.0
HD22 A:LEU30 3.0 27.6 1.0
H2 A:71Q301 3.1 26.9 1.0
C5 A:71Q301 3.1 26.3 1.0
C2 A:71Q301 3.3 27.8 1.0
CG2 A:ILE75 3.4 14.5 1.0
H1 A:71Q301 3.5 28.2 1.0
HD21 A:LEU78 3.6 22.7 1.0
CD2 A:LEU63 3.7 21.0 1.0
HD23 A:LEU63 3.7 21.4 1.0
CG1 A:ILE75 3.9 14.2 1.0
HG22 A:ILE75 3.9 13.4 1.0
HD21 A:LEU63 3.9 21.1 1.0
HG23 A:ILE75 4.0 15.9 1.0
CB A:ILE75 4.0 13.5 1.0
HB A:ILE75 4.1 12.9 1.0
HD12 A:ILE75 4.1 20.5 1.0
HD13 A:LEU30 4.1 23.1 1.0
HD22 A:LEU78 4.1 22.5 1.0
CD2 A:LEU30 4.1 27.4 1.0
CD2 A:LEU78 4.2 22.8 1.0
HD23 A:LEU78 4.2 22.9 1.0
HB2 A:LEU30 4.4 16.2 1.0
C6 A:71Q301 4.4 25.7 1.0
HE21 A:GLN120 4.5 16.1 0.5
CD1 A:ILE75 4.5 19.7 1.0
C1 A:71Q301 4.5 28.3 1.0
HD21 A:LEU30 4.6 28.1 1.0
HD21 A:LEU176 4.6 18.2 1.0
HD23 A:LEU30 4.6 27.5 1.0
CL A:CL308 4.6 14.1 1.0
HD11 A:LEU176 4.7 19.5 1.0
HG12 A:ILE75 4.7 14.4 1.0
HD11 A:ILE75 4.8 19.3 1.0
C A:71Q301 4.9 27.9 1.0
CG A:LEU30 4.9 22.8 1.0
HB3 A:LEU30 4.9 15.3 1.0
HH2 A:TRP145 5.0 15.5 1.0
CD1 A:LEU30 5.0 24.1 1.0
HD13 A:LEU63 5.0 19.7 1.0

Fluorine binding site 3 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 3 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:33.1
occ:1.00
F2 A:71Q301 0.0 33.1 1.0
C4 A:71Q301 1.3 30.0 1.0
F1 A:71Q301 2.1 27.7 1.0
F A:71Q301 2.1 28.6 1.0
C3 A:71Q301 2.4 27.7 1.0
H1 A:71Q301 2.4 28.2 1.0
C2 A:71Q301 2.8 27.8 1.0
CL A:CL308 3.0 14.1 1.0
HD22 A:LEU30 3.2 27.6 1.0
HD21 A:LEU176 3.2 18.2 1.0
HG A:SER119 3.5 13.3 1.0
C5 A:71Q301 3.6 26.3 1.0
HB2 A:LEU30 3.7 16.2 1.0
HB3 A:LEU30 3.9 15.3 1.0
H2 A:71Q301 3.9 26.9 1.0
O B:HOH414 4.0 13.1 1.0
HD23 A:LEU176 4.1 17.3 1.0
CD2 A:LEU176 4.1 18.1 1.0
C1 A:71Q301 4.1 28.3 1.0
CD2 A:LEU30 4.1 27.4 1.0
HG A:LEU176 4.2 16.6 1.0
HG13 A:ILE75 4.2 15.2 1.0
HD23 A:LEU30 4.2 27.5 1.0
CB A:LEU30 4.3 15.1 1.0
HE21 A:GLN120 4.3 16.1 0.5
HD11 A:LEU176 4.3 19.5 1.0
HG21 A:ILE75 4.3 14.9 1.0
OG A:SER119 4.3 12.6 1.0
HH2 A:TRP145 4.5 15.5 1.0
HD13 A:LEU30 4.6 23.1 1.0
CG A:LEU176 4.6 17.8 1.0
H A:LEU30 4.7 13.8 1.0
HB3 A:GLN120 4.7 13.1 0.5
HB3 A:GLN120 4.7 14.2 0.5
CG A:LEU30 4.8 22.8 1.0
C6 A:71Q301 4.8 25.7 1.0
H A:GLN120 4.8 8.2 0.5
H A:GLN120 4.8 8.2 0.5
HD22 A:LEU78 4.9 22.5 1.0
HZ3 A:TRP145 4.9 13.3 1.0
HD22 A:LEU63 4.9 21.1 1.0
C A:71Q301 5.0 27.9 1.0
HD21 A:LEU78 5.0 22.7 1.0
HD21 A:LEU30 5.0 28.1 1.0
HD22 A:LEU176 5.0 18.1 1.0

Fluorine binding site 4 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 4 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:22.2
occ:1.00
F B:71Q301 0.0 22.2 1.0
C4 B:71Q301 1.3 24.3 1.0
F2 B:71Q301 2.1 27.5 1.0
F1 B:71Q301 2.1 26.1 1.0
C3 B:71Q301 2.4 22.6 1.0
HG13 B:ILE75 2.6 16.7 1.0
H2 B:71Q301 2.6 19.1 1.0
HD22 B:LEU30 2.9 28.7 1.0
C5 B:71Q301 2.9 18.5 1.0
HH2 B:TRP145 3.1 14.4 1.0
HD11 B:ILE75 3.1 18.2 1.0
HG21 B:ILE75 3.2 16.3 1.0
HB3 B:GLN120 3.2 12.3 0.5
HD12 B:ILE75 3.2 18.0 1.0
CG1 B:ILE75 3.4 16.2 1.0
CL B:CL303 3.4 14.0 1.0
HB2 B:GLN120 3.4 11.3 0.5
CD1 B:ILE75 3.4 18.3 1.0
C2 B:71Q301 3.5 25.8 1.0
HB2 B:LEU30 3.7 15.6 1.0
HE21 B:GLN120 3.8 24.4 0.5
H1 B:71Q301 3.8 26.1 1.0
CD2 B:LEU30 3.9 28.2 1.0
CH2 B:TRP145 4.0 13.3 1.0
CG2 B:ILE75 4.1 16.2 1.0
HD23 B:LEU30 4.1 27.5 1.0
HG B:SER119 4.2 12.2 1.0
HG12 B:ILE75 4.2 16.7 1.0
C6 B:71Q301 4.2 21.0 1.0
CB B:ILE75 4.3 16.7 1.0
CB B:GLN120 4.3 12.0 0.5
HG23 B:ILE75 4.3 15.3 1.0
HG2 B:GLN120 4.3 14.4 0.5
HD13 B:LEU30 4.4 24.9 1.0
H B:GLN120 4.5 10.4 0.5
HD21 B:LEU30 4.5 28.6 1.0
H B:GLN120 4.5 10.2 0.5
CB B:GLN120 4.5 10.0 0.5
HZ3 B:TRP145 4.5 12.6 1.0
HD13 B:ILE75 4.5 19.2 1.0
NE2 B:GLN120 4.6 24.0 0.5
CB B:LEU30 4.6 14.8 1.0
HB B:ILE75 4.6 16.6 1.0
HB3 B:LEU30 4.7 14.1 1.0
C1 B:71Q301 4.7 26.5 1.0
CZ3 B:TRP145 4.7 12.8 1.0
CG B:LEU30 4.7 22.8 1.0
CG B:GLN120 4.8 14.5 0.5
O2 B:71Q301 4.8 18.4 1.0
HZ2 B:TRP145 4.8 15.0 1.0
HB2 B:GLN120 4.8 12.0 0.5
HD22 B:LEU63 4.8 23.7 1.0
HG3 B:GLN120 4.9 10.2 0.5
CZ2 B:TRP145 4.9 13.7 1.0
HA B:GLN120 4.9 7.9 0.5
HE21 B:GLN120 4.9 12.7 0.5
NE2 B:GLN120 4.9 11.9 0.5
HG22 B:ILE75 4.9 17.4 1.0
H B:LEU30 5.0 14.4 1.0
C B:71Q301 5.0 26.9 1.0
OG B:SER119 5.0 12.0 1.0

Fluorine binding site 5 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 5 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:26.1
occ:1.00
F1 B:71Q301 0.0 26.1 1.0
C4 B:71Q301 1.3 24.3 1.0
F2 B:71Q301 2.1 27.5 1.0
F B:71Q301 2.1 22.2 1.0
HG21 B:ILE75 2.3 16.3 1.0
C3 B:71Q301 2.3 22.6 1.0
HD22 B:LEU63 2.9 23.7 1.0
HD22 B:LEU30 2.9 28.7 1.0
HG13 B:ILE75 3.0 16.7 1.0
H2 B:71Q301 3.1 19.1 1.0
C5 B:71Q301 3.1 18.5 1.0
C2 B:71Q301 3.3 25.8 1.0
CG2 B:ILE75 3.4 16.2 1.0
H1 B:71Q301 3.5 26.1 1.0
HD21 B:LEU78 3.5 25.4 1.0
HD23 B:LEU30 3.6 27.5 1.0
CD2 B:LEU30 3.6 28.2 1.0
CD2 B:LEU63 3.7 23.6 1.0
HG22 B:ILE75 3.9 17.4 1.0
HD21 B:LEU30 3.9 28.6 1.0
HD21 B:LEU63 3.9 23.7 1.0
CG1 B:ILE75 3.9 16.2 1.0
HD23 B:LEU63 3.9 24.1 1.0
HG23 B:ILE75 4.0 15.3 1.0
CB B:ILE75 4.0 16.7 1.0
HB B:ILE75 4.0 16.6 1.0
HD12 B:ILE75 4.1 18.0 1.0
CD2 B:LEU78 4.2 25.1 1.0
HD23 B:LEU78 4.2 24.7 1.0
HD22 B:LEU78 4.2 25.4 1.0
HD11 B:LEU176 4.2 19.1 1.0
C6 B:71Q301 4.3 21.0 1.0
HD21 B:LEU176 4.4 17.4 1.0
C1 B:71Q301 4.4 26.5 1.0
CD1 B:ILE75 4.5 18.3 1.0
HD11 B:ILE75 4.7 18.2 1.0
HB2 B:LEU30 4.7 15.6 1.0
HD13 B:LEU63 4.7 22.9 1.0
HG12 B:ILE75 4.8 16.7 1.0
C B:71Q301 4.9 26.9 1.0
CL B:CL303 4.9 14.0 1.0
HB3 B:LEU63 4.9 16.2 1.0
HH2 B:TRP145 5.0 14.4 1.0
CG B:LEU30 5.0 22.8 1.0

Fluorine binding site 6 out of 6 in 5sym

Go back to Fluorine Binding Sites List in 5sym
Fluorine binding site 6 out of 6 in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:27.5
occ:1.00
F2 B:71Q301 0.0 27.5 1.0
C4 B:71Q301 1.3 24.3 1.0
F1 B:71Q301 2.1 26.1 1.0
F B:71Q301 2.1 22.2 1.0
C3 B:71Q301 2.4 22.6 1.0
H1 B:71Q301 2.4 26.1 1.0
C2 B:71Q301 2.7 25.8 1.0
HD21 B:LEU176 3.0 17.4 1.0
HD22 B:LEU30 3.1 28.7 1.0
CL B:CL303 3.2 14.0 1.0
HD23 B:LEU30 3.4 27.5 1.0
HG B:SER119 3.6 12.2 1.0
C5 B:71Q301 3.6 18.5 1.0
CD2 B:LEU30 3.7 28.2 1.0
HB2 B:LEU30 3.8 15.6 1.0
HD11 B:LEU176 3.9 19.1 1.0
CD2 B:LEU176 3.9 16.7 1.0
H2 B:71Q301 3.9 19.1 1.0
HB3 B:LEU30 4.0 14.1 1.0
HG B:LEU176 4.1 17.5 1.0
HD23 B:LEU176 4.1 16.7 1.0
C1 B:71Q301 4.1 26.5 1.0
HG13 B:ILE75 4.2 16.7 1.0
HG21 B:ILE75 4.3 16.3 1.0
O A:HOH420 4.4 21.2 1.0
CB B:LEU30 4.4 14.8 1.0
OG B:SER119 4.4 12.0 1.0
CG B:LEU176 4.4 17.2 1.0
HH2 B:TRP145 4.5 14.4 1.0
HD21 B:LEU30 4.5 28.6 1.0
CD1 B:LEU176 4.7 19.1 1.0
HB2 B:GLN120 4.7 11.3 0.5
HD22 B:LEU176 4.7 17.1 1.0
HB3 B:GLN120 4.7 12.3 0.5
CG B:LEU30 4.7 22.8 1.0
C6 B:71Q301 4.8 21.0 1.0
H B:LEU30 4.8 14.4 1.0
HD22 B:LEU63 4.9 23.7 1.0
HZ3 B:TRP145 4.9 12.6 1.0
H B:GLN120 4.9 10.4 0.5
HD21 B:LEU78 4.9 25.4 1.0
C B:71Q301 4.9 26.9 1.0
H B:GLN120 5.0 10.2 0.5

Reference:

S.J.Won, D.Davda, K.J.Labby, S.Y.Hwang, R.Pricer, J.D.Majmudar, K.A.Armacost, L.A.Rodriguez, C.L.Rodriguez, F.S.Chong, K.A.Torossian, J.Palakurthi, E.S.Hur, J.L.Meagher, C.L.Brooks, J.A.Stuckey, B.R.Martin. Molecular Mechanism For Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). Acs Chem. Biol. V. 11 3374 2016.
ISSN: ESSN 1554-8937
PubMed: 27748579
DOI: 10.1021/ACSCHEMBIO.6B00720
Page generated: Tue Jul 15 07:44:47 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy