SMTL ID : 6qgv.1

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with a Spiro[4.5]decanone inhibitor (JPHM-2-167)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.139, D.141, H.200 Ligands: J2H.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 J2H: 8-[(3-methylpyridin-2-yl)methyl]-3-(4-phenylphenyl)-1-pyrimidin-2-yl-1,3,8-triazaspiro[4.5]decane-2,4-dione(Non-covalent)

J2H.2: 20 residues within 4Å: Chain A: I.82, W.84, T.122, M.125, Y.129, Y.136, H.139, D.141, D.146, R.148, I.153, L.169, F.192, H.200, V.202, R.209, W.215, F.217, R.222 Ligands: MN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.84, A:T.122, A:Y.136, A:V.202, A:W.215, A:F.217, A:F.217 Hydrogen bonds: A:R.148 Water bridges: A:R.148 Salt bridges: A:D.141 pi-Stacking: A:W.215 pi-Cation interactions: A:R.148

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.176, A.177, Q.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.177, A:Q.178, A:Q.178 Water bridges: A:G.175

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 8 residues within 4Å: Chain A: D.103, I.106, R.107, I.118, N.119, G.120, R.121, Y.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.107 Hydrogen bonds: A:I.118

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

SO4.5: 3 residues within 4Å: Chain A: P.90, G.91, E.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.91, A:E.93 SO4.6: 3 residues within 4Å: Chain A: R.170, D.181, Q.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.181, A:Q.203 Salt bridges: A:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holt-Martyn, J.P. et al., Studies on spiro[4.5]decanone prolyl hydroxylase domain inhibitors. Medchemcomm (2019)

Release Date

2020-02-05

Peptides

Egl nine homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Egl nine homolog 1

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