SMTL ID : 6rj3.1

Crystal structure of PHGDH in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.53, S.54, R.74 Chain B: R.134 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.54 Water bridges: A:A.55, A:A.55, A:Q.291, A:Q.291 Salt bridges: A:R.53, A:R.74, B:R.134 SO4.3: 5 residues within 4Å: Chain A: R.134 Chain B: R.53, S.54, R.74, A.285 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Salt bridges: A:R.134, B:R.53, B:R.74, B:H.282 Hydrogen bonds: B:S.54 Water bridges: B:R.74, B:T.77, B:H.282, B:A.285, B:Q.291, B:Q.291

2 x K58: 4-[(1~{R})-1-[(2-methyl-5-phenyl-pyrazol-3-yl)carbonylamino]ethyl]benzoic acid(Non-covalent)

K58.2: 16 residues within 4Å: Chain A: L.150, G.151, G.153, I.155, Y.173, D.174, P.175, I.176, I.177, L.192, H.205, 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, A:L.215 Hydrogen bonds: A:D.174 K58.4: 14 residues within 4Å: Chain B: L.150, G.151, G.153, Y.173, D.174, P.175, I.176, I.177, H.205, T.206, P.207, L.209, T.212, L.215 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.173, B:I.177, B:T.206, B:T.212, B:L.215, B:L.215 Hydrogen bonds: B:D.174

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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