SMTL ID : 6plf.1

Crystal structure of human PHGDH complexed with Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ONV: 4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid(Non-covalent)

ONV.1: 14 residues within 4Å: Chain A: G.151, G.153, Y.173, D.174, P.175, I.176, I.177, L.192, H.205, T.206, P.207, S.211, T.212, L.215 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.206, A:T.212 Hydrogen bonds: A:D.174 ONV.5: 14 residues within 4Å: Chain B: G.151, R.154, Y.173, D.174, P.175, I.176, I.177, L.192, H.205, T.206, P.207, S.211, T.212, L.215 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.175, B:T.206, B:P.207, B:T.212 Hydrogen bonds: B:D.174 Salt bridges: B:R.154 pi-Cation interactions: B:R.154

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: E.241, F.261, P.266, D.268, R.269, A.270, L.271, V.272 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.241, A:R.269, A:L.271, A:V.272 Water bridges: A:T.262, A:T.262, A:D.268 EDO.3: 4 residues within 4Å: Chain A: K.169, T.170, G.186, Q.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.170, A:Q.188 Water bridges: A:G.186, A:V.187 EDO.4: 7 residues within 4Å: Chain A: C.115, L.116, Q.119, Q.122, R.229, A.254, N.276 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.122, A:R.229, A:R.229 Water bridges: A:Q.119, A:Q.119 EDO.6: 8 residues within 4Å: Chain B: E.241, F.261, P.266, D.268, R.269, A.270, L.271, V.272 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.241, B:R.269, B:L.271, B:V.272 Water bridges: B:T.262, B:A.270 EDO.7: 7 residues within 4Å: Chain B: L.116, Q.119, Q.122, R.229, A.254, G.255, N.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.122, B:R.229, B:R.229

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
B

D-3-phosphoglycerate dehydrogenase

Related Entries With Identical Sequence