Chlorine in PDB 6plg: Crystal Structure of Human Phgdh Complexed with Compound 15

All present enzymatic activity of Crystal Structure of Human Phgdh Complexed with Compound 15:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Crystal Structure of Human Phgdh Complexed with Compound 15, PDB code: 6plg was solved by A.Olland, D.Lakshminarasimhan, A.White, R.K.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 2.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.649, 112.699, 137.840, 105.98, 96.20, 101.42
R / Rfree (%)	27.4 / 31.5

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Phgdh Complexed with Compound 15 (pdb code 6plg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Crystal Structure of Human Phgdh Complexed with Compound 15, PDB code: 6plg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:0.9 occ:1.00 CL A:ONS401 0.0 0.9 1.0 C3 A:ONS401 1.8 80.7 1.0 C2 A:ONS401 2.7 83.0 1.0 C4 A:ONS401 2.8 81.6 1.0 CL1 A:ONS401 2.8 93.1 1.0 C7 A:ONS401 3.3 80.3 1.0 CD A:PRO176 3.4 72.7 1.0 O A:TYR174 3.6 72.5 1.0 CG2 A:THR207 3.7 82.1 1.0 CA A:ASP175 3.9 72.7 1.0 CD2 A:TYR174 4.0 74.1 1.0 C1 A:ONS401 4.0 83.2 1.0 C5 A:ONS401 4.1 81.7 1.0 CE2 A:TYR174 4.2 74.4 1.0 N A:GLY152 4.2 72.2 1.0 CB A:ASP175 4.4 72.5 1.0 C A:TYR174 4.4 72.9 1.0 CA A:GLY152 4.4 72.2 1.0 CG A:PRO176 4.4 73.0 1.0 N A:PRO176 4.6 72.9 1.0 C A:LEU151 4.6 72.3 1.0 C A:ONS401 4.6 79.5 1.0 N A:ASP175 4.6 73.1 1.0 OD2 A:ASP175 4.6 72.9 1.0 C6 A:ONS401 4.7 79.2 1.0 CG A:ASP175 4.7 72.7 1.0 C A:ASP175 4.8 72.9 1.0 CB A:THR207 4.9 82.5 1.0 N A:ONS401 5.0 82.1 1.0

Chlorine binding site 2 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:93.1 occ:1.00 CL1 A:ONS401 0.0 93.1 1.0 C2 A:ONS401 1.8 83.0 1.0 C3 A:ONS401 2.6 80.7 1.0 C1 A:ONS401 2.8 83.2 1.0 CL A:ONS401 2.8 0.9 1.0 C4 A:ONS401 4.0 81.6 1.0 CE2 A:TYR174 4.1 74.4 1.0 C A:ONS401 4.1 79.5 1.0 CD1 A:LEU216 4.1 90.1 1.0 CD2 A:LEU216 4.2 89.3 1.0 CD2 A:TYR174 4.4 74.1 1.0 C5 A:ONS401 4.5 81.7 1.0 O A:SER212 4.5 94.8 1.0 CD A:PRO176 4.6 72.7 1.0 CB A:THR213 4.8 91.7 1.0 CG A:LEU216 4.8 90.1 1.0 OG1 A:THR213 4.8 91.4 1.0 CG A:PRO176 4.9 73.0 1.0 CA A:THR213 5.0 93.1 1.0

Chlorine binding site 3 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:90.8 occ:1.00 CL B:ONS401 0.0 90.8 1.0 C3 B:ONS401 1.8 80.5 1.0 C2 B:ONS401 2.7 83.4 1.0 C4 B:ONS401 2.8 82.4 1.0 CL1 B:ONS401 3.0 91.4 1.0 C7 B:ONS401 3.3 80.2 1.0 CG2 B:THR207 3.5 82.1 1.0 CD B:PRO176 3.6 74.4 1.0 O B:TYR174 3.6 75.4 1.0 CA B:ASP175 3.9 75.2 1.0 CD2 B:TYR174 4.0 77.0 1.0 C1 B:ONS401 4.0 84.3 1.0 C5 B:ONS401 4.1 83.7 1.0 N B:GLY152 4.1 75.2 1.0 CA B:GLY152 4.2 75.2 1.0 CE2 B:TYR174 4.3 77.2 1.0 CB B:ASP175 4.3 75.1 1.0 C B:TYR174 4.4 75.9 1.0 C B:LEU151 4.4 75.2 1.0 N B:ASP175 4.6 75.8 1.0 C B:ONS401 4.6 80.9 1.0 CG B:PRO176 4.6 74.5 1.0 C6 B:ONS401 4.6 75.9 1.0 OD2 B:ASP175 4.6 75.5 1.0 N B:PRO176 4.7 74.8 1.0 CG B:ASP175 4.7 75.3 1.0 CB B:THR207 4.7 82.3 1.0 C B:ASP175 4.9 75.2 1.0 O B:LEU151 4.9 75.2 1.0 CA B:LEU151 4.9 75.5 1.0 N B:ONS401 5.0 82.4 1.0 CB B:LEU151 5.0 75.7 1.0

Chlorine binding site 4 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:91.4 occ:1.00 CL1 B:ONS401 0.0 91.4 1.0 C2 B:ONS401 1.8 83.4 1.0 C3 B:ONS401 2.7 80.5 1.0 C1 B:ONS401 2.8 84.3 1.0 CL B:ONS401 3.0 90.8 1.0 CE2 B:TYR174 4.0 77.2 1.0 CD2 B:LEU216 4.0 90.8 1.0 C4 B:ONS401 4.0 82.4 1.0 OG1 B:THR213 4.1 93.9 1.0 C B:ONS401 4.1 80.9 1.0 O B:SER212 4.2 98.0 1.0 CD2 B:TYR174 4.3 77.0 1.0 C5 B:ONS401 4.6 83.7 1.0 CD B:PRO176 4.6 74.4 1.0 CD1 B:LEU216 4.8 91.9 1.0 CG B:PRO176 4.9 74.5 1.0 CD1 B:LEU193 4.9 82.5 1.0 C B:SER212 5.0 96.1 1.0

Chlorine binding site 5 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:88.0 occ:1.00 CL C:ONS401 0.0 88.0 1.0 C3 C:ONS401 1.8 79.2 1.0 C4 C:ONS401 2.8 77.4 1.0 C2 C:ONS401 2.8 75.3 1.0 O C:TYR174 2.9 89.0 1.0 CL1 C:ONS401 3.2 82.9 1.0 C7 C:ONS401 3.2 76.4 1.0 CA C:ASP175 3.5 91.1 1.0 N C:GLY152 3.6 82.2 1.0 CD C:PRO176 3.7 90.9 1.0 CD2 C:TYR174 3.7 92.5 1.0 C C:TYR174 3.7 90.5 1.0 CG2 C:THR207 3.8 81.9 1.0 CB C:ASP175 3.9 89.5 1.0 CA C:GLY152 3.9 82.8 1.0 C C:LEU151 4.0 80.5 1.0 N C:ASP175 4.0 91.5 1.0 C5 C:ONS401 4.1 74.0 1.0 C1 C:ONS401 4.1 73.4 1.0 CE2 C:TYR174 4.2 93.4 1.0 OD2 C:ASP175 4.4 88.2 1.0 CA C:LEU151 4.4 79.9 1.0 CG C:ASP175 4.4 90.1 1.0 C C:ONS401 4.6 74.4 1.0 N C:PRO176 4.6 92.3 1.0 C6 C:ONS401 4.6 71.5 1.0 C C:ASP175 4.6 93.1 1.0 CB C:LEU151 4.7 78.6 1.0 CG C:TYR174 4.7 93.4 1.0 O C:LEU151 4.7 79.8 1.0 CG C:PRO176 4.8 91.7 1.0 CB C:TYR174 4.9 92.4 1.0 CA C:TYR174 4.9 92.2 1.0 N C:ONS401 4.9 72.2 1.0

Chlorine binding site 6 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:82.9 occ:1.00 CL1 C:ONS401 0.0 82.9 1.0 C2 C:ONS401 1.8 75.3 1.0 C3 C:ONS401 2.7 79.2 1.0 C1 C:ONS401 2.8 73.4 1.0 CL C:ONS401 3.2 88.0 1.0 CD2 C:LEU216 3.6 81.5 1.0 CE2 C:TYR174 3.7 93.4 1.0 CD2 C:TYR174 3.8 92.5 1.0 C4 C:ONS401 4.0 77.4 1.0 C C:ONS401 4.1 74.4 1.0 CD1 C:LEU193 4.3 0.3 1.0 OG1 C:THR213 4.5 94.2 1.0 C5 C:ONS401 4.6 74.0 1.0 CD1 C:LEU216 4.7 82.9 1.0 O C:SER212 4.7 95.7 1.0 CG C:LEU216 4.8 81.6 1.0 CD C:PRO176 4.8 90.9 1.0 CZ C:TYR174 4.9 95.2 1.0 CG C:LEU193 5.0 0.6 1.0 CG2 C:THR207 5.0 81.9 1.0

Chlorine binding site 7 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:0.4 occ:1.00 CL D:ONS401 0.0 0.4 1.0 C3 D:ONS401 1.8 87.0 1.0 C2 D:ONS401 2.7 86.4 1.0 C4 D:ONS401 2.8 85.8 1.0 CL1 D:ONS401 3.1 93.6 1.0 O D:TYR174 3.2 87.8 1.0 C7 D:ONS401 3.3 82.0 1.0 CD D:PRO176 3.3 94.3 1.0 CD1 D:TYR174 3.5 92.2 1.0 CA D:ASP175 3.6 92.6 1.0 CG2 D:THR207 3.9 83.8 1.0 CE1 D:TYR174 3.9 93.2 1.0 C D:TYR174 3.9 89.6 1.0 C1 D:ONS401 4.0 86.4 1.0 N D:GLY152 4.0 80.2 1.0 CB D:ASP175 4.1 92.3 1.0 C5 D:ONS401 4.1 84.6 1.0 N D:ASP175 4.1 91.7 1.0 CA D:GLY152 4.3 81.0 1.0 N D:PRO176 4.4 95.4 1.0 C D:LEU151 4.4 78.4 1.0 CG D:PRO176 4.5 95.3 1.0 CG D:ASP175 4.5 93.1 1.0 C D:ASP175 4.5 95.3 1.0 OD2 D:ASP175 4.5 92.4 1.0 C D:ONS401 4.5 86.4 1.0 C6 D:ONS401 4.6 77.0 1.0 CG D:TYR174 4.6 92.1 1.0 CA D:LEU151 4.8 77.8 1.0 N D:ONS401 5.0 80.0 1.0 CB D:LEU151 5.0 76.7 1.0 CB D:TYR174 5.0 90.9 1.0

Chlorine binding site 8 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:93.6 occ:1.00 CL1 D:ONS401 0.0 93.6 1.0 C2 D:ONS401 1.8 86.4 1.0 C3 D:ONS401 2.8 87.0 1.0 C1 D:ONS401 2.8 86.4 1.0 CL D:ONS401 3.1 0.4 1.0 CD2 D:LEU216 3.6 82.1 1.0 CE1 D:TYR174 4.0 93.2 1.0 C4 D:ONS401 4.1 85.8 1.0 C D:ONS401 4.1 86.4 1.0 CD1 D:TYR174 4.2 92.2 1.0 OG1 D:THR213 4.3 86.4 1.0 CD1 D:LEU193 4.4 0.6 1.0 O D:SER212 4.5 93.7 1.0 C5 D:ONS401 4.6 84.6 1.0 CD1 D:LEU216 4.7 83.3 1.0 CG D:LEU216 4.8 82.4 1.0 CD D:PRO176 4.9 94.3 1.0 CG2 D:THR207 5.0 83.8 1.0

Chlorine binding site 9 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl401 b:0.9 occ:1.00 CL E:ONS401 0.0 0.9 1.0 C3 E:ONS401 1.8 0.3 1.0 C2 E:ONS401 2.7 0.5 1.0 C4 E:ONS401 2.8 1.0 1.0 CL1 E:ONS401 3.0 0.4 1.0 CG2 E:THR207 3.1 97.1 1.0 C7 E:ONS401 3.4 0.1 1.0 O E:TYR174 3.6 91.5 1.0 N E:GLY152 3.8 88.2 1.0 C E:LEU151 4.0 88.1 1.0 CD E:PRO176 4.0 99.4 1.0 C1 E:ONS401 4.0 0.9 1.0 CA E:GLY152 4.0 89.3 1.0 C5 E:ONS401 4.1 0.4 1.0 CD2 E:TYR174 4.2 92.9 1.0 CA E:ASP175 4.3 94.7 1.0 O E:LEU151 4.4 88.9 1.0 CB E:THR207 4.4 98.5 1.0 CA E:LEU151 4.4 87.3 1.0 C E:TYR174 4.5 91.6 1.0 CB E:LEU151 4.5 87.9 1.0 C E:ONS401 4.6 0.6 1.0 CB E:ASP175 4.6 94.8 1.0 CE2 E:TYR174 4.6 93.8 1.0 CD2 E:LEU216 4.6 94.3 1.0 C6 E:ONS401 4.7 0.9 1.0 N E:ASP175 4.8 93.0 1.0 OG1 E:THR213 4.9 99.6 1.0 CG E:PRO176 5.0 0.7 1.0 N E:ONS401 5.0 1.0 1.0

Chlorine binding site 10 out of 16 in the Crystal Structure of Human Phgdh Complexed with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Human Phgdh Complexed with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl401 b:0.4 occ:1.00 CL1 E:ONS401 0.0 0.4 1.0 C2 E:ONS401 1.8 0.5 1.0 C3 E:ONS401 2.7 0.3 1.0 C1 E:ONS401 2.8 0.9 1.0 CL E:ONS401 3.0 0.9 1.0 CD2 E:LEU216 3.3 94.3 1.0 CD1 E:LEU216 3.8 95.6 1.0 C4 E:ONS401 4.0 1.0 1.0 C E:ONS401 4.1 0.6 1.0 CE2 E:TYR174 4.1 93.8 1.0 O E:SER212 4.1 99.1 1.0 OG1 E:THR213 4.1 99.6 1.0 CG E:LEU216 4.2 94.9 1.0 CD2 E:TYR174 4.2 92.9 1.0 C5 E:ONS401 4.5 0.4 1.0 CD1 E:LEU193 4.7 95.7 1.0 CD E:PRO176 4.8 99.4 1.0 CA E:THR213 4.9 0.7 1.0 C E:SER212 4.9 0.8 1.0 CG2 E:THR207 5.0 97.1 1.0

E.Mullarky, J.Xu, A.D.Robin, D.J.Huggins, A.Jennings, N.Noguchi, A.Olland, D.Lakshminarasimhan, M.Miller, D.Tomita, M.Michino, T.Su, G.Zhang, A.W.Stamford, P.T.Meinke, S.Kargman, L.C.Cantley. Inhibition of 3-Phosphoglycerate Dehydrogenase (Phgdh) By Indole Amides Abrogates De Novo Serine Synthesis in Cancer Cells. Bioorg.Med.Chem.Lett. V. 29 2503 2019.
ISSN: ESSN 1464-3405
PubMed: 31327531
DOI: 10.1016/J.BMCL.2019.07.011