SMTL ID : 5opc.1

Factor Inhibiting HIF (FIH) in complex with zinc and Vadadustat

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: I.136, R.139, G.141, E.142, E.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.142, A:E.143 Salt bridges: A:R.139 SO4.2: 5 residues within 4Å: Chain A: D.223, K.312, A.313, H.314 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.313 SO4.3: 5 residues within 4Å: Chain A: K.108, V.233, D.238, R.321, K.325 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.238, A:D.238 Water bridges: A:K.108, A:K.108 Salt bridges: A:K.108, A:R.321, A:K.325 SO4.4: 7 residues within 4Å: Chain A: R.34, R.144, E.193, G.194, L.286, N.287 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.193, A:E.193, A:N.287 Salt bridges: A:R.144 SO4.5: 3 residues within 4Å: Chain A: R.18, R.45, T.66 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.45 SO4.13: 5 residues within 4Å: Chain B: I.136, R.139, G.141, E.142, E.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.142, B:E.143 Salt bridges: B:R.139 SO4.14: 5 residues within 4Å: Chain B: D.223, K.312, A.313, H.314 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.313 SO4.15: 5 residues within 4Å: Chain B: K.108, V.233, D.238, R.321, K.325 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.238 Water bridges: B:K.108, B:K.108 Salt bridges: B:K.108, B:R.321, B:K.325 SO4.16: 7 residues within 4Å: Chain B: R.34, R.144, E.193, G.194, L.286, N.287 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.193, B:N.287 Salt bridges: B:R.144 SO4.17: 3 residues within 4Å: Chain B: R.18, R.45, T.66 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.45

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.200, D.202, H.280, W.297 Ligands: A1Z.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.200, A:D.202, A:H.280 ZN.18: 5 residues within 4Å: Chain B: H.200, D.202, H.280, W.297 Ligands: A1Z.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.200, B:D.202, B:H.280

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: K.100, L.102, P.198, Y.231, S.241, Q.242, V.243, D.244, F.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.231, A:Q.242 GOL.8: 8 residues within 4Å: Chain A: Y.103, T.197, H.200, D.202, D.238, R.239, Q.240 Ligands: A1Z.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.238, A:R.239, A:R.239 GOL.9: 6 residues within 4Å: Chain A: E.61, P.221, D.223, Y.262, W.278 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.61, A:D.223, A:Y.262 GOL.10: 5 residues within 4Å: Chain A: R.34, T.98, H.99, R.144 Ligands: SO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:R.34, A:H.99, A:H.99, A:R.144, A:R.144 GOL.11: 4 residues within 4Å: Chain A: W.168, N.169, N.172, K.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.168, A:N.172 GOL.19: 9 residues within 4Å: Chain B: K.100, L.102, P.198, Y.231, S.241, Q.242, V.243, D.244, F.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.231, B:Q.242 GOL.20: 8 residues within 4Å: Chain B: Y.103, T.197, H.200, D.202, D.238, R.239, Q.240 Ligands: A1Z.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.238, B:R.239, B:R.239 GOL.21: 6 residues within 4Å: Chain B: E.61, P.221, D.223, Y.262, W.278 Ligands: SO4.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.61, B:D.223, B:Y.262 GOL.22: 5 residues within 4Å: Chain B: R.34, T.98, H.99, R.144 Ligands: SO4.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.34, B:R.34, B:H.99, B:H.99, B:R.144, B:R.144 GOL.23: 4 residues within 4Å: Chain B: W.168, N.169, N.172, K.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.168, B:N.172

2 x A1Z: Vadadustat(Non-covalent)

A1Z.12: 17 residues within 4Å: Chain A: Y.146, Q.148, S.185, L.187, L.189, T.197, H.200, D.202, F.208, K.215, R.239, H.280, I.282, N.295, W.297 Ligands: ZN.6, GOL.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.187, A:W.297, A:W.297 Hydrogen bonds: A:Y.146, A:Q.148, A:N.295 Water bridges: A:Y.146 Salt bridges: A:K.215 pi-Stacking: A:W.297 A1Z.24: 17 residues within 4Å: Chain B: Y.146, Q.148, S.185, L.187, L.189, T.197, H.200, D.202, F.208, K.215, R.239, H.280, I.282, N.295, W.297 Ligands: ZN.18, GOL.20 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.187, B:W.297, B:W.297 Hydrogen bonds: B:Y.146, B:Q.148, B:N.295 Water bridges: B:Y.146 Salt bridges: B:K.215 pi-Stacking: B:W.297

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

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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