SMTL ID : 6rj2.1

Crystal structure of PHGDH in complex with compound 40

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.53, S.54, R.74 Chain B: R.134, K.135 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.54, A:S.54 Salt bridges: A:R.53, A:R.74, B:R.134, B:K.135

2 x K52: ~{N}-[(1~{R})-1-[4-(ethanoylsulfamoyl)phenyl]ethyl]-2-methyl-5-phenyl-pyrazole-3-carboxamide(Non-covalent)

K52.2: 18 residues within 4Å: Chain A: N.99, S.102, 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, T.212, L.215, R.235 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.155, A:Y.173, A:I.177, A:T.206, A:T.212, A:L.215, A:L.215 Hydrogen bonds: A:R.154, A:I.155, A:D.174, A:R.235, A:R.235 Water bridges: A:G.156 K52.3: 16 residues within 4Å: Chain B: S.102, 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, T.212, L.215 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.154, B:I.155, B:Y.173, B:I.177, B:T.206, B:T.212, B:L.215, B:L.215 Hydrogen bonds: B:R.154, B:I.155, B:D.174 Water bridges: B:G.156

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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