SMTL ID : 6cwa.1

CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.1: 12 residues within 4Å: Chain A: R.66, S.67, R.87, A.88, G.89, T.90, N.114, R.248, H.295, A.298 Chain B: R.147 Ligands: NAI.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.67, A:T.90, A:N.114, A:R.248, A:R.248 Water bridges: A:R.87, A:R.87, A:R.87, A:A.88, B:R.147 Salt bridges: A:R.66, A:R.87, A:R.87, A:R.248, A:H.295, B:R.147 3PG.3: 12 residues within 4Å: Chain A: R.147 Chain B: R.66, S.67, R.87, G.89, T.90, G.91, N.114, R.248, H.295, A.298 Ligands: NAI.4 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Salt bridges: A:R.147, B:R.66, B:R.87, B:R.87, B:R.248, B:H.295 Hydrogen bonds: B:S.67, B:S.67, B:R.87, B:A.88, B:T.90, B:T.90, B:G.91, B:N.114, B:R.248, B:R.248 Water bridges: B:R.66, B:A.68

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 25 residues within 4Å: Chain A: T.90, N.114, A.118, G.164, G.166, R.167, I.168, Y.186, D.187, P.188, I.189, H.218, T.219, P.220, S.224, T.225, C.246, A.247, R.248, D.272, V.273, H.295, G.297, A.298 Ligands: 3PG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.118, A:I.168 Hydrogen bonds: A:G.166, A:R.167, A:I.168, A:T.219, A:S.224, A:C.246, A:D.272, A:G.297, A:A.298 Water bridges: A:T.90, A:G.169, A:R.248 Salt bridges: A:R.167 NAI.4: 24 residues within 4Å: Chain B: T.90, N.114, A.118, G.164, G.166, R.167, I.168, Y.186, D.187, P.188, I.189, H.218, T.219, P.220, T.225, C.246, A.247, R.248, D.272, V.273, H.295, G.297, A.298 Ligands: 3PG.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.118, B:I.168 Hydrogen bonds: B:G.166, B:R.167, B:I.168, B:T.219, B:S.224, B:C.246, B:G.297, B:A.298 Water bridges: B:R.167, B:R.167, B:G.169, B:R.248, B:R.248 Salt bridges: B:R.167

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