SMTL ID : 5ox6.1

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Vadadustat

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.139, D.141, F.192, H.200 Ligands: A1Z.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.139, A:D.141, A:H.200, H2O.1

1 x A1Z: Vadadustat(Non-covalent)

A1Z.2: 18 residues within 4Å: Chain A: D.80, I.82, W.84, M.125, A.127, Y.129, Y.136, H.139, D.141, I.153, Y.155, L.169, H.200, V.202, R.209, A.211, W.215 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.129, A:Y.129, A:Y.129, A:Y.155 Salt bridges: A:R.209 pi-Stacking: A:Y.136

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

SO4.3: 1 residues within 4Å: Chain A: R.222 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.222 SO4.4: 4 residues within 4Å: Chain A: I.182, E.183, K.185, R.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.183, A:E.183 Salt bridges: A:R.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: L.113, G.114, S.115, Y.116, W.193, R.197 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.115, A:S.115, A:R.197, A:R.197 Water bridges: A:G.114 GOL.6: 4 residues within 4Å: Chain A: R.138, H.139, V.140, P.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.138, A:R.138, A:R.138 Water bridges: A:V.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeh, T.L. et al., Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci (2017)

Release Date

2017-10-18

Peptides

Egl nine homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Egl nine homolog 1

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