SMTL ID : 6rih.1

Crystal structure of PHGDH in complex with compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x K4T: ~{N}-cyclopropyl-2-methyl-5-phenyl-pyrazole-3-carboxamide(Non-covalent)

K4T.1: 14 residues within 4Å: Chain A: L.150, G.151, G.153, Y.173, D.174, P.175, I.176, I.177, L.192, T.206, P.207, L.209, T.212, L.215 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.150, A:Y.173, A:I.177, A:L.192, A:T.206, A:T.212, A:L.215 Hydrogen bonds: A:D.174 Water bridges: A:S.211 K4T.3: 14 residues within 4Å: Chain B: L.150, G.151, G.153, Y.173, D.174, P.175, I.176, I.177, L.192, T.206, P.207, L.209, T.212, L.215 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.173, B:I.176, B:I.177, B:L.192, B:T.206, B:T.212, B:L.215 Hydrogen bonds: B:D.174

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.134 Chain B: R.53, S.54, R.74, A.285 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.54, B:S.54 Water bridges: B:T.77, B:H.282, B:A.285, B:Q.291, B:Q.291 Salt bridges: B:R.53, B:R.74, B:H.282, A:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinstabl, H. et al., Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis. J.Med.Chem. (2019)

Release Date

2019-08-07

Peptides

D-3-phosphoglycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-phosphoglycerate dehydrogenase

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