Chlorine 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:

Fluorine

(F)

6 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Cocrystal Structure of the Human Acyl Protein Thioesterase 1 with An Isoform-Selective Inhibitor, ML348, PDB code: 5sym:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301 b:27.9 occ:1.00 CL A:71Q301 0.0 27.9 1.0 C A:71Q301 1.7 27.9 1.0 C1 A:71Q301 2.7 28.3 1.0 C6 A:71Q301 2.7 25.7 1.0 N A:71Q301 2.9 25.0 1.0 HD2 A:PHE181 3.0 20.0 1.0 HE2 A:PHE181 3.1 23.5 1.0 HA A:VAL177 3.2 11.8 1.0 HB3 A:LEU78 3.4 14.8 1.0 HA A:LEU78 3.4 14.4 1.0 HG13 A:VAL177 3.4 13.9 1.0 HG22 A:VAL177 3.5 15.9 1.0 HD2 A:PRO178 3.7 13.2 1.0 O A:LEU78 3.7 21.9 1.0 CD2 A:PHE181 3.8 20.1 1.0 CE2 A:PHE181 3.8 23.7 1.0 O A:LEU176 3.9 18.2 1.0 HD22 A:LEU78 3.9 22.5 1.0 C2 A:71Q301 4.0 27.8 1.0 N1 A:71Q301 4.0 20.4 1.0 C5 A:71Q301 4.0 26.3 1.0 H15 A:71Q301 4.0 22.4 1.0 H9 A:71Q301 4.0 23.2 1.0 O A:HOH411 4.0 33.2 1.0 C16 A:71Q301 4.1 22.0 1.0 HD3 A:PRO178 4.1 15.5 1.0 CA A:LEU78 4.1 15.1 1.0 CB A:LEU78 4.2 15.7 1.0 C7 A:71Q301 4.2 23.2 1.0 CA A:VAL177 4.3 11.9 1.0 C17 A:71Q301 4.3 21.6 1.0 HD23 A:LEU78 4.3 22.9 1.0 C A:LEU78 4.3 20.7 1.0 CD A:PRO178 4.4 15.0 1.0 CG1 A:VAL177 4.4 14.2 1.0 CG2 A:VAL177 4.4 14.9 1.0 C3 A:71Q301 4.5 27.7 1.0 CD2 A:LEU78 4.5 22.8 1.0 CB A:VAL177 4.6 14.9 1.0 C8 A:71Q301 4.7 20.5 1.0 C10 A:71Q301 4.7 22.9 1.0 C A:LEU176 4.8 18.9 1.0 H1 A:71Q301 4.8 28.2 1.0 CE3 A:TRP145 4.8 11.0 1.0 HE3 A:TRP145 4.9 11.5 1.0 HG23 A:VAL177 4.9 14.5 1.0 H2 A:71Q301 4.9 26.9 1.0 C9 A:71Q301 4.9 19.2 1.0 N2 A:71Q301 4.9 22.1 1.0 O A:HOH454 4.9 29.0 1.0 N A:VAL177 5.0 13.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl307 b:16.0 occ:1.00 H A:ALA20 2.3 12.7 1.0 O2 A:EDO305 2.9 38.3 1.0 HA A:LYS19 3.0 12.8 1.0 O A:HOH511 3.2 16.3 1.0 N A:ALA20 3.3 12.4 1.0 HB3 A:ALA20 3.3 13.9 1.0 O1 A:EDO305 3.5 33.6 1.0 HG3 A:LYS19 3.5 14.2 1.0 HB2 A:ALA20 3.7 12.4 1.0 CB A:ALA20 3.9 12.2 1.0 CA A:LYS19 4.0 11.5 1.0 C1 A:EDO305 4.0 37.6 1.0 HB3 A:ALA16 4.0 14.0 1.0 C2 A:EDO305 4.0 38.6 1.0 HD2 A:LYS50 4.1 17.1 1.0 C A:LYS19 4.1 15.4 1.0 CA A:ALA20 4.2 12.1 1.0 CG A:LYS19 4.4 13.7 1.0 HB2 A:LYS50 4.6 15.6 1.0 H A:ALA16 4.6 13.7 1.0 HG2 A:LYS19 4.6 13.2 1.0 CB A:LYS19 4.8 14.1 1.0 N A:LYS19 4.9 11.8 1.0 HD11 A:ILE108 4.9 17.9 1.0 HB1 A:ALA20 4.9 11.8 1.0 HA A:ALA20 4.9 12.0 1.0 O A:ARG18 4.9 14.4 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl308 b:14.1 occ:1.00 HG A:SER119 2.1 13.3 1.0 H A:LEU30 2.2 13.8 1.0 H A:GLN120 2.3 8.2 0.5 H A:GLN120 2.3 8.2 0.5 HG2 A:GLN120 2.5 13.1 0.5 HG2 A:GLN120 2.6 24.5 0.5 HB2 A:LEU30 2.8 16.2 1.0 HB3 A:SER119 2.8 11.6 1.0 O B:HOH414 3.0 13.1 1.0 OG A:SER119 3.0 12.6 1.0 F2 A:71Q301 3.0 33.1 1.0 HB3 A:GLN120 3.0 13.1 0.5 HB3 A:GLN120 3.1 14.2 0.5 HE21 A:GLN120 3.1 16.1 0.5 F A:71Q301 3.1 28.6 1.0 N A:LEU30 3.2 12.3 1.0 HB3 A:LEU30 3.2 15.3 1.0 N A:GLN120 3.3 9.2 1.0 CG A:GLN120 3.4 12.5 0.5 CB A:SER119 3.4 11.5 1.0 CB A:LEU30 3.4 15.1 1.0 CG A:GLN120 3.5 23.9 0.5 CB A:GLN120 3.6 11.5 0.5 CB A:GLN120 3.7 12.7 0.5 C4 A:71Q301 3.7 30.0 1.0 HA3 A:GLY29 3.7 9.5 1.0 HA2 A:GLY29 3.8 12.9 1.0 NE2 A:GLN120 3.9 16.1 0.5 CA A:LEU30 3.9 13.3 1.0 CA A:GLN120 4.0 8.8 0.5 CA A:GLN120 4.1 9.4 0.5 CD A:GLN120 4.1 14.6 0.5 HH2 A:TRP145 4.1 15.5 1.0 HG3 A:GLN120 4.1 23.5 0.5 CA A:GLY29 4.2 10.2 1.0 C A:GLY29 4.2 13.9 1.0 HG3 A:GLN120 4.2 12.1 0.5 HB2 A:SER119 4.2 11.0 1.0 C A:SER119 4.2 10.4 1.0 CA A:SER119 4.4 8.5 1.0 HZ3 A:TRP145 4.4 13.3 1.0 CD A:GLN120 4.4 26.5 0.5 HD22 A:LEU30 4.5 27.6 1.0 HA A:LEU30 4.5 13.7 1.0 C3 A:71Q301 4.6 27.7 1.0 HB2 A:GLN120 4.6 11.9 0.5 HA A:GLN120 4.6 9.8 0.5 F1 A:71Q301 4.6 27.7 1.0 H A:GLY121 4.7 9.2 1.0 HA A:GLN120 4.7 10.4 0.5 HB2 A:GLN120 4.7 13.3 0.5 CG A:LEU30 4.7 22.8 1.0 HE22 A:GLN120 4.7 16.2 0.5 HD13 A:LEU30 4.7 23.1 1.0 H1 A:71Q301 4.8 28.2 1.0 NE2 A:HIS208 4.9 13.6 1.0 HA A:SER119 4.9 9.6 1.0 CH2 A:TRP145 5.0 13.1 1.0 HE21 A:GLN120 5.0 16.5 0.5 O A:PHE118 5.0 9.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 A:Cl309 b:21.1 occ:1.00 H A:ILE229 2.0 18.4 1.0 HH22 A:ARG18 2.1 18.2 1.0 HH12 A:ARG18 2.3 25.1 1.0 HA A:PRO228 2.8 17.4 1.0 HG21 A:THR21 2.9 13.1 1.0 OG1 A:THR21 2.9 14.3 1.0 N A:ILE229 3.0 18.1 1.0 NH2 A:ARG18 3.0 18.8 1.0 HG1 A:THR21 3.1 13.9 1.0 HG12 A:ILE229 3.1 24.9 1.0 HB2 A:HIS48 3.2 11.7 1.0 NH1 A:ARG18 3.2 24.2 1.0 HG13 A:ILE229 3.2 25.6 1.0 O A:ILE229 3.3 26.8 1.0 CZ A:ARG18 3.5 30.6 1.0 CG2 A:THR21 3.5 11.8 1.0 CA A:PRO228 3.6 16.3 1.0 HB3 A:PRO228 3.6 20.1 1.0 CG1 A:ILE229 3.6 25.2 1.0 HB3 A:HIS48 3.6 10.3 1.0 HG23 A:THR21 3.6 11.2 1.0 CB A:HIS48 3.7 10.2 1.0 CB A:THR21 3.7 12.8 1.0 CG A:HIS48 3.7 13.2 1.0 C A:PRO228 3.7 19.2 1.0 HH21 A:ARG18 3.8 18.6 1.0 CA A:ILE229 3.9 20.1 1.0 HH22 A:ARG112 3.9 13.6 1.0 CD2 A:HIS48 4.0 13.6 1.0 C A:ILE229 4.0 26.5 1.0 HH21 A:ARG112 4.0 14.5 1.0 HH11 A:ARG18 4.0 24.5 1.0 HB A:THR21 4.0 13.1 1.0 CB A:PRO228 4.1 19.1 1.0 HD2 A:HIS48 4.2 13.4 1.0 NH2 A:ARG112 4.3 13.5 1.0 ND1 A:HIS48 4.3 14.3 1.0 CB A:ILE229 4.4 23.9 1.0 HG22 A:THR21 4.5 10.6 1.0 HB2 A:PRO228 4.6 20.2 1.0 NE2 A:HIS48 4.7 14.0 1.0 HG23 A:ILE229 4.7 24.4 1.0 O A:PRO227 4.7 14.1 1.0 CE1 A:HIS48 4.8 14.2 1.0 NE A:ARG18 4.8 23.5 1.0 HD11 A:ILE229 4.9 35.1 1.0 N A:PRO228 4.9 14.7 1.0 HA A:ILE229 4.9 20.5 1.0 H A:THR21 4.9 10.7 1.0 CD1 A:ILE229 4.9 35.3 1.0 O A:PRO228 4.9 16.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301 b:31.8 occ:1.00 CL B:71Q301 0.0 31.8 1.0 C B:71Q301 1.7 26.9 1.0 C1 B:71Q301 2.7 26.5 1.0 C6 B:71Q301 2.7 21.0 1.0 HE2 B:PHE181 2.8 28.8 1.0 HD2 B:PHE181 2.9 24.3 1.0 N B:71Q301 2.9 20.9 1.0 H8 B:71Q301 3.2 18.1 1.0 HA B:VAL177 3.2 9.9 1.0 HG13 B:VAL177 3.4 13.9 1.0 HA B:LEU78 3.4 19.7 1.0 CE2 B:PHE181 3.5 28.4 1.0 HB3 B:LEU78 3.5 19.3 1.0 CD2 B:PHE181 3.6 25.3 1.0 HG22 B:VAL177 3.6 13.8 1.0 HD2 B:PRO178 3.7 16.7 1.0 HD22 B:LEU78 3.7 25.4 1.0 O B:LEU78 3.8 25.4 1.0 O B:LEU176 3.9 18.6 1.0 C2 B:71Q301 4.0 25.8 1.0 C5 B:71Q301 4.0 18.5 1.0 HD3 B:PRO178 4.1 17.9 1.0 N1 B:71Q301 4.1 21.2 1.0 H6 B:71Q301 4.1 19.0 1.0 CA B:LEU78 4.2 18.8 1.0 C10 B:71Q301 4.2 18.1 1.0 O B:HOH424 4.2 42.4 1.0 C7 B:71Q301 4.3 21.1 1.0 CA B:VAL177 4.3 11.5 1.0 CB B:LEU78 4.3 19.2 1.0 CD B:PRO178 4.4 16.7 1.0 HD23 B:LEU78 4.4 24.7 1.0 C B:LEU78 4.4 24.4 1.0 C9 B:71Q301 4.4 19.5 1.0 CG1 B:VAL177 4.4 12.4 1.0 CD2 B:LEU78 4.5 25.1 1.0 CG2 B:VAL177 4.5 13.2 1.0 C3 B:71Q301 4.5 22.6 1.0 CB B:VAL177 4.6 13.1 1.0 H9 B:71Q301 4.8 17.8 1.0 CZ B:PHE181 4.8 27.8 1.0 C8 B:71Q301 4.8 22.5 1.0 C B:LEU176 4.8 16.9 1.0 H1 B:71Q301 4.8 26.1 1.0 C16 B:71Q301 4.8 20.2 1.0 O B:HOH496 4.9 27.7 1.0 CG B:PHE181 4.9 22.0 1.0 HG23 B:VAL177 4.9 13.8 1.0 H2 B:71Q301 4.9 19.1 1.0 HG12 B:VAL177 5.0 12.7 1.0 N B:VAL177 5.0 12.3 1.0 C17 B:71Q301 5.0 21.8 1.0 N2 B:71Q301 5.0 20.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl303 b:14.0 occ:1.00 HG B:SER119 2.1 12.2 1.0 H B:LEU30 2.1 14.4 1.0 H B:GLN120 2.2 10.4 0.5 H B:GLN120 2.2 10.2 0.5 HG2 B:GLN120 2.5 14.4 0.5 HB2 B:LEU30 2.6 15.6 1.0 HB2 B:GLN120 2.8 11.3 0.5 HB3 B:SER119 2.8 9.4 1.0 O A:HOH420 3.0 21.2 1.0 OG B:SER119 3.0 12.0 1.0 N B:LEU30 3.1 12.5 1.0 N B:GLN120 3.2 9.5 1.0 F2 B:71Q301 3.2 27.5 1.0 HB3 B:GLN120 3.2 12.3 0.5 HB3 B:LEU30 3.3 14.1 1.0 CB B:LEU30 3.4 14.8 1.0 HB3 B:GLN120 3.4 9.4 0.5 CB B:SER119 3.4 9.3 1.0 F B:71Q301 3.4 22.2 1.0 CB B:GLN120 3.5 10.0 0.5 CG B:GLN120 3.5 14.5 0.5 HA3 B:GLY29 3.7 12.0 1.0 HA2 B:GLY29 3.7 9.9 1.0 CB B:GLN120 3.7 12.0 0.5 CA B:LEU30 3.9 12.9 1.0 C4 B:71Q301 3.9 24.3 1.0 CA B:GLN120 3.9 8.8 0.5 CA B:GLN120 4.0 9.8 0.5 CA B:GLY29 4.0 10.8 1.0 C B:GLY29 4.1 12.4 1.0 HD22 B:LEU30 4.1 28.7 1.0 HG3 B:GLN120 4.1 14.4 0.5 C B:SER119 4.2 10.7 1.0 HB2 B:SER119 4.2 7.9 1.0 HH2 B:TRP145 4.2 14.4 1.0 CA B:SER119 4.4 8.9 1.0 HA B:GLN120 4.4 7.9 0.5 CD B:GLN120 4.5 22.8 0.5 HZ3 B:TRP145 4.5 12.6 1.0 HD23 B:LEU30 4.6 27.5 1.0 HA B:LEU30 4.6 11.9 1.0 CG B:LEU30 4.6 22.8 1.0 CD2 B:LEU30 4.6 28.2 1.0 HA B:GLN120 4.6 9.4 0.5 HE21 B:GLN120 4.7 24.4 0.5 HD13 B:LEU30 4.7 24.9 1.0 H B:GLY121 4.7 10.8 1.0 C3 B:71Q301 4.7 22.6 1.0 HB2 B:GLN120 4.8 12.0 0.5 CG B:GLN120 4.8 10.5 0.5 H1 B:71Q301 4.8 26.1 1.0 NE2 B:HIS208 4.9 13.2 1.0 NE2 B:GLN120 4.9 24.0 0.5 O B:PHE118 4.9 9.1 1.0 F1 B:71Q301 4.9 26.1 1.0 HD21 B:LEU176 4.9 17.4 1.0 CD B:GLN120 5.0 17.4 0.5 HA B:SER119 5.0 9.3 1.0

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