SMTL ID : 4jzr.1

Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.130, D.132, H.191 Ligands: 4JR.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.130, A:D.132, A:H.191, H2O.2

1 x 4JR: 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one(Non-covalent)

4JR.2: 15 residues within 4Å: Chain A: W.75, T.113, Y.120, Y.127, H.130, D.132, R.139, L.160, H.191, V.193, W.206, F.208, R.213 Ligands: NI.1, EDO.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.75, A:T.113, A:W.206, A:F.208 Hydrogen bonds: A:R.139, A:R.139 Salt bridges: A:D.132 pi-Stacking: A:Y.127, A:W.206 pi-Cation interactions: A:R.139

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: Y.120, I.144, Y.146, L.160, V.193, R.200, A.202 Ligands: 4JR.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.200, A:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, G. et al., Novel complex crystal structure of prolyl hydroxylase domain-containing protein 2 (PHD2): 2,8-Diazaspiro[4.5]decan-1-ones as potent, orally bioavailable PHD2 inhibitors. Bioorg.Med.Chem. (2013)

Release Date

2013-10-30

Peptides

Egl nine homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Egl nine homolog 1