SMTL ID : 6plg.1 (3 other biounits)

Crystal structure of human PHGDH complexed with Compound 15

Coordinates

PDB Format Compare

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: 16 residues within 4Å: Chain A: L.152, 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, A.234, R.235 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.175, A:L.209, A:A.234 Hydrogen bonds: A:R.154, A:I.155, A:D.174, A:R.235 Halogen bonds: A:Y.173 ONS.2: 19 residues within 4Å: Chain B: L.150, G.151, 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.155, B:P.175, B:T.206 Hydrogen bonds: B:R.154, B:R.154, B:I.155, B:D.174, B:R.235 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, A.75, G.76, T.77, N.101, H.282, A.285, Q.291 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.285 Hydrogen bonds: B:S.54, B:A.75, B:T.77, B:H.282, B:Q.291, A:R.134, A:R.134 Salt bridges: B:R.53, B:R.74, 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
A

B
E

D-3-phosphoglycerate dehydrogenase

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