SMTL ID : 7a1k.1

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-((9,9-dimethyl-9H-fluoren-2-yl)methyl)-2-oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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: QVZ.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.199, A:D.201, A:H.279, H2O.1 ZN.7: 5 residues within 4Å: Chain B: H.199, D.201, H.279, W.296 Ligands: QVZ.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.199, B:D.201, B:H.279, H2O.3

2 x QVZ: 3-((9,9-dimethyl-9H-fluoren-2-yl)methyl)-2-oxoglutarate(Non-covalent)

QVZ.2: 20 residues within 4Å: Chain A: Y.93, F.100, L.101, Y.102, Y.103, Y.145, Q.147, L.186, L.188, T.196, H.199, D.201, N.205, F.207, K.214, H.279, I.281, N.294, W.296 Ligands: ZN.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.93, A:Y.102, A:Y.145, A:Q.147, A:L.186, A:L.188, A:L.188, A:F.207, A:I.281 Hydrogen bonds: A:Y.145, A:T.196, A:T.196, A:N.205, A:N.294, A:W.296 Salt bridges: A:K.214, A:H.279 pi-Cation interactions: A:H.199 QVZ.8: 20 residues within 4Å: Chain B: Y.93, F.100, L.101, Y.102, Y.103, Y.145, Q.147, L.186, L.188, T.196, H.199, D.201, N.205, F.207, K.214, H.279, I.281, N.294, W.296 Ligands: ZN.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.93, B:Y.102, B:Y.145, B:Q.147, B:L.186, B:L.188, B:L.188, B:F.207, B:I.281 Hydrogen bonds: B:Y.145, B:T.196, B:T.196, B:N.205, B:N.294, B:W.296 Salt bridges: B:K.214, B:H.279 pi-Cation interactions: B:H.199

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

SO4.3: 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 SO4.4: 6 residues within 4Å: Chain A: R.33, R.143, E.192, G.193, L.285, N.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33, A:N.286 Water bridges: A:R.33 Salt bridges: A:R.143 SO4.5: 4 residues within 4Å: Chain A: P.221, D.222, K.311, A.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.312 Water bridges: A:H.313, A:H.313 SO4.6: 6 residues within 4Å: Chain A: K.107, E.202, V.232, D.237, R.320, K.324 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.237, A:D.237 Salt bridges: A:K.107, A:R.320, A:K.324 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.33, B:N.286 Water bridges: B:R.33 Salt bridges: B:R.143 SO4.11: 4 residues within 4Å: Chain B: P.221, D.222, K.311, A.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.312 Water bridges: B:H.313, B:H.313 SO4.12: 6 residues within 4Å: Chain B: K.107, E.202, V.232, D.237, R.320, K.324 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.237 Salt bridges: B:K.107, B:R.320, B:K.324

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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