SMTL ID : 6plg.4 (3 other biounits)

Crystal structure of human PHGDH complexed with Compound 15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-dimer

Ligands

2 x ONS: (2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid(Non-covalent)

ONS.1: 17 residues within 4Å: Chain A: G.153, R.154, I.155, Y.173, D.174, P.175, I.176, I.177, H.205, T.206, P.207, L.209, S.211, T.212, L.215, A.234, R.235 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.175, A:H.205, A:T.206 Hydrogen bonds: A:R.154, A:I.155, A:D.174 Halogen bonds: A:Y.173 ONS.2: 17 residues within 4Å: Chain B: T.77, G.153, R.154, I.155, Y.173, D.174, P.175, I.176, I.177, H.205, T.206, P.207, L.209, S.211, T.212, L.215, A.234 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.206, B:A.234 Hydrogen bonds: B:R.154, B:I.155, B:D.174 Halogen bonds: B:Y.173

1 x MLT: D-MALATE(Non-covalent)

MLT.3: 11 residues within 4Å: Chain A: R.134 Chain B: R.53, S.54, R.74, G.76, T.77, N.101, R.235, H.282, A.285, Q.291 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.285 Hydrogen bonds: B:S.54, B:R.74, B:T.77, B:H.282 Salt bridges: B:R.53, B:R.74, B:R.235, B:H.282, A:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullarky, E. et al., Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells. Bioorg.Med.Chem.Lett. (2019)

Release Date

2019-07-24

Peptides

D-3-phosphoglycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

D-3-phosphoglycerate dehydrogenase

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