SMTL ID : 7a1j.1

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-(3-phenylpropyl)-2-oxoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.199, D.201, H.279, W.296 Ligands: QVN.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.199, A:D.201, A:H.279, H2O.3 ZN.8: 5 residues within 4Å: Chain B: H.199, D.201, H.279, W.296 Ligands: QVN.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.199, B:D.201, B:H.279, H2O.10

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

SO4.2: 4 residues within 4Å: Chain A: R.138, G.140, E.141, E.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.141, A:E.142 Salt bridges: A:R.138 SO4.3: 6 residues within 4Å: Chain A: R.33, R.143, E.192, G.193, L.285, N.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.33, A:N.286 Water bridges: A:R.143, A:R.143 Salt bridges: A:R.143 SO4.4: 4 residues within 4Å: Chain A: P.221, D.222, K.311, A.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.312 Water bridges: A:H.313 SO4.5: 2 residues within 4Å: Chain A: R.120, E.122 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.120 SO4.6: 3 residues within 4Å: Chain A: Q.148, T.149, N.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.148 Water bridges: A:N.151 SO4.9: 4 residues within 4Å: Chain B: R.138, G.140, E.141, E.142 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.141, B:E.142 Salt bridges: B:R.138 SO4.10: 6 residues within 4Å: Chain B: R.33, R.143, E.192, G.193, L.285, N.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.33, B:N.286 Water bridges: B:R.143, B:R.143 Salt bridges: B:R.143 SO4.11: 4 residues within 4Å: Chain B: P.221, D.222, K.311, A.312 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.312 Water bridges: B:H.313 SO4.12: 2 residues within 4Å: Chain B: R.120, E.122 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.120 SO4.13: 3 residues within 4Å: Chain B: Q.148, T.149, N.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.148 Water bridges: B:N.151

2 x QVN: 3-(3-phenylpropyl)-2-oxoglutarate(Non-covalent)

QVN.7: 18 residues within 4Å: Chain A: Y.102, Y.145, Q.147, L.186, L.188, T.196, H.199, D.201, N.205, F.207, K.214, R.238, Q.239, H.279, I.281, N.294, W.296 Ligands: ZN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.102, A:L.188, A:L.188, A:F.207 Hydrogen bonds: A:Y.145, A:T.196, A:T.196, A:N.205, A:N.294, A:W.296 Water bridges: A:D.201 Salt bridges: A:K.214, A:H.279 pi-Stacking: A:Y.102 QVN.14: 18 residues within 4Å: Chain B: Y.102, Y.145, Q.147, L.186, L.188, T.196, H.199, D.201, N.205, F.207, K.214, R.238, Q.239, H.279, I.281, N.294, W.296 Ligands: ZN.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.102, B:L.188, B:L.188, B:F.207 Hydrogen bonds: B:Y.145, B:T.196, B:T.196, B:N.205, B:N.294, B:W.296 Water bridges: B:D.201 Salt bridges: B:K.214, B:H.279 pi-Stacking: B:Y.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, Y. et al., 2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases. Nat Commun (2021)

Release Date

2021-08-25

Peptides

Hypoxia-inducible factor 1-alpha inhibitor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypoxia-inducible factor 1-alpha inhibitor

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