SMTL ID : 7ewh.1

Crystal structure of human PHGDH in complex with Homoharringtonine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-dimer

Ligands

2 x HMT: (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine(Non-covalent)

HMT.1: 16 residues within 4Å: Chain A: I.145, L.146, G.147, L.148, G.149, R.150, I.151, G.152, D.170, P.171, I.172, V.200, H.201, T.202, P.203, T.208 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.150, A:I.151, A:P.203 Hydrogen bonds: A:R.150, A:D.170, A:H.201, A:T.202 Water bridges: A:T.202 HMT.2: 13 residues within 4Å: Chain B: I.145, L.146, G.147, L.148, G.149, R.150, I.151, G.152, D.170, P.171, H.201, T.202, P.203 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.150, B:H.201 Hydrogen bonds: B:L.148, B:G.149, B:D.170, B:H.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, C.H. et al., Homoharringtonine as a PHGDH inhibitor: Unraveling metabolic dependencies and developing a potent therapeutic strategy for high-risk neuroblastoma. Biomed Pharmacother (2023)

Release Date

2022-12-07

Peptides

D-3-phosphoglycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-phosphoglycerate dehydrogenase