Chlorine in PDB 6rj6: Crystal Structure of Phgdh in Complex with Bi-4924

All present enzymatic activity of Crystal Structure of Phgdh in Complex with Bi-4924:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Crystal Structure of Phgdh in Complex with Bi-4924, PDB code: 6rj6 was solved by G.Bader, B.Wolkerstorfer, A.Zoephel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.137, 111.959, 62.505, 90.00, 90.99, 90.00
R / Rfree (%)	26.2 / 29.8

The binding sites of Chlorine atom in the Crystal Structure of Phgdh in Complex with Bi-4924 (pdb code 6rj6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Phgdh in Complex with Bi-4924, PDB code: 6rj6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Phgdh in Complex with Bi-4924


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 Phgdh in Complex with Bi-4924 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:17.9 occ:1.00 CL1 A:K5K401 0.0 17.9 1.0 C4 A:K5K401 1.7 20.7 1.0 C5 A:K5K401 2.7 21.4 1.0 C1 A:K5K401 2.7 22.7 1.0 CL2 A:K5K401 3.1 25.6 1.0 C9 A:K5K401 3.3 22.1 1.0 N A:GLY151 3.3 12.7 1.0 O A:TYR173 3.4 13.7 1.0 CG2 A:THR206 3.6 12.0 1.0 CD2 A:TYR173 3.7 13.4 1.0 CA A:GLY151 3.8 13.2 1.0 C A:LEU150 3.8 14.4 1.0 C6 A:K5K401 4.0 21.1 1.0 C2 A:K5K401 4.0 22.9 1.0 C A:TYR173 4.1 14.1 1.0 CA A:ASP174 4.1 12.0 1.0 CA A:LEU150 4.2 11.1 1.0 CE2 A:TYR173 4.2 13.7 1.0 CD A:PRO175 4.2 14.9 1.0 CB A:LEU150 4.3 11.1 1.0 N A:ASP174 4.4 11.8 1.0 O A:LEU150 4.5 12.9 1.0 C3 A:K5K401 4.5 21.7 1.0 C8 A:K5K401 4.6 22.6 1.0 OD2 A:ASP174 4.7 16.5 1.0 CG A:TYR173 4.7 13.3 1.0 CB A:THR206 4.7 14.1 1.0 CB A:ASP174 4.9 12.5 1.0 CB A:TYR173 4.9 12.0 1.0 N7 A:K5K401 4.9 21.2 1.0 CD2 A:LEU215 5.0 22.5 1.0 CG A:ASP174 5.0 16.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Phgdh in Complex with Bi-4924


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 Phgdh in Complex with Bi-4924 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:25.6 occ:1.00 CL2 A:K5K401 0.0 25.6 1.0 C1 A:K5K401 1.7 22.7 1.0 C2 A:K5K401 2.7 22.9 1.0 C4 A:K5K401 2.7 20.7 1.0 C14 A:K5K401 3.1 23.0 1.0 CL1 A:K5K401 3.1 17.9 1.0 CD1 A:LEU215 3.5 20.6 1.0 CE2 A:TYR173 3.6 13.7 1.0 CD2 A:TYR173 3.6 13.4 1.0 CD1 A:LEU192 3.8 31.9 1.0 C3 A:K5K401 4.0 21.7 1.0 CD2 A:LEU215 4.0 22.5 1.0 CD2 A:LEU192 4.0 33.1 1.0 C5 A:K5K401 4.0 21.4 1.0 CG A:LEU215 4.3 20.0 1.0 CG A:LEU192 4.4 31.3 1.0 C6 A:K5K401 4.5 21.1 1.0 CZ A:TYR173 4.8 20.1 1.0 CG A:TYR173 4.9 13.3 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Phgdh in Complex with Bi-4924


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 Phgdh in Complex with Bi-4924 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:20.7 occ:1.00 CL1 B:K5K401 0.0 20.7 1.0 C4 B:K5K401 1.7 19.6 1.0 C5 B:K5K401 2.7 19.4 1.0 C1 B:K5K401 2.7 19.1 1.0 CL2 B:K5K401 3.1 20.1 1.0 O B:TYR173 3.3 15.5 1.0 C9 B:K5K401 3.3 20.3 1.0 CG2 B:THR206 3.4 11.9 1.0 N B:GLY151 3.6 10.2 1.0 C6 B:K5K401 4.0 19.5 1.0 CA B:GLY151 4.0 10.4 1.0 CD2 B:TYR173 4.0 16.6 1.0 C2 B:K5K401 4.0 18.8 1.0 C B:LEU150 4.0 12.0 1.0 C B:TYR173 4.0 16.4 1.0 CD B:PRO175 4.0 18.6 1.0 CA B:ASP174 4.1 13.8 1.0 N B:ASP174 4.4 13.6 1.0 C3 B:K5K401 4.5 19.5 1.0 CA B:LEU150 4.5 9.3 1.0 CB B:LEU150 4.5 9.4 1.0 O B:LEU150 4.6 11.3 1.0 CE2 B:TYR173 4.6 18.5 1.0 C8 B:K5K401 4.6 20.9 1.0 OD2 B:ASP174 4.6 31.6 1.0 CB B:THR206 4.8 15.9 1.0 CB B:ASP174 4.8 15.2 1.0 CG B:ASP174 4.9 27.8 1.0 CG B:TYR173 4.9 15.8 1.0 CD2 B:LEU215 4.9 20.4 1.0 N7 B:K5K401 4.9 20.9 1.0 CB B:TYR173 5.0 13.6 1.0 N B:PRO175 5.0 16.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Phgdh in Complex with Bi-4924


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 Phgdh in Complex with Bi-4924 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:20.1 occ:1.00 CL2 B:K5K401 0.0 20.1 1.0 C1 B:K5K401 1.7 19.1 1.0 C2 B:K5K401 2.7 18.8 1.0 C4 B:K5K401 2.7 19.6 1.0 C14 B:K5K401 3.1 18.6 1.0 CL1 B:K5K401 3.1 20.7 1.0 CD1 B:LEU215 3.6 20.5 1.0 CD2 B:TYR173 3.8 16.6 1.0 CE2 B:TYR173 3.9 18.5 1.0 C3 B:K5K401 4.0 19.5 1.0 CD2 B:LEU192 4.0 20.6 1.0 CD2 B:LEU215 4.0 20.4 1.0 C5 B:K5K401 4.0 19.4 1.0 CD1 B:LEU192 4.3 16.7 1.0 CG B:LEU215 4.4 19.5 1.0 C6 B:K5K401 4.5 19.5 1.0 CG B:LEU192 4.8 17.4 1.0 CD B:PRO175 4.9 18.6 1.0

H.Weinstabl, M.Treu, J.Rinnenthal, S.K.Zahn, P.Ettmayer, G.Bader, G.Dahmann, D.Kessler, K.Rumpel, N.Mischerikow, F.Savarese, T.Gerstberger, M.Mayer, A.Zoephel, R.Schnitzer, W.Sommergruber, P.Martinelli, H.Arnhof, B.Peric-Simov, K.S.Hofbauer, G.Garavel, Y.Scherbantin, S.Mitzner, T.N.Fett, G.Scholz, J.Bruchhaus, M.Burkard, R.Kousek, T.Ciftci, B.Sharps, A.Schrenk, C.Harrer, D.Haering, B.Wolkerstorfer, X.Zhang, X.Lv, A.Du, D.Li, Y.Li, J.Quant, M.Pearson, D.B.Mcconnell. Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (Phgdh) Inhibitorbi-4924DISRUPTS Serine Biosynthesis. J.Med.Chem. V. 62 7976 2019.
ISSN: ISSN 0022-2623
PubMed: 31365252
DOI: 10.1021/ACS.JMEDCHEM.9B00718