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

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

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

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 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 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 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 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 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 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

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