SMTL ID : 8k71.1

Factor-inhibiting hypoxia-inducible factor in complex with Zn(II) and 2-(3-hydroxy-2-((2-((naphthalen-2-ylmethyl)sulfonyl)acetyl)imino)-2,3-dihydrothiazol-4-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.199, D.201, H.279 Ligands: VIZ.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.199, A:D.201, A:H.279 ZN.18: 4 residues within 4Å: Chain B: H.199, D.201, H.279 Ligands: VIZ.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.199, B:D.201, B:H.279

2 x VIZ: 2-[(2~{Z})-2-[2-(naphthalen-2-ylmethylsulfonyl)ethanoylimino]-3-oxidanyl-1,3-thiazol-4-yl]ethanoic acid(Non-covalent)

VIZ.2: 17 residues within 4Å: Chain A: Y.145, Q.147, T.183, S.184, L.186, L.188, T.196, H.199, D.201, Q.203, F.207, K.214, R.238, H.279, I.281, W.296 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.196, A:D.201, A:Q.203, A:I.281, A:W.296, A:W.296 Hydrogen bonds: A:Y.145 Salt bridges: A:K.214 pi-Stacking: A:W.296 VIZ.19: 17 residues within 4Å: Chain B: Y.145, Q.147, T.183, S.184, L.186, L.188, T.196, H.199, D.201, Q.203, F.207, K.214, R.238, H.279, I.281, W.296 Ligands: ZN.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.196, B:D.201, B:Q.203, B:I.281, B:W.296, B:W.296 Hydrogen bonds: B:T.196 Salt bridges: B:K.214 pi-Stacking: B:W.296

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

SO4.3: 4 residues within 4Å: Chain A: R.138, G.140, E.141, E.142 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: K.311, A.312 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: G.155, R.156 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.143, E.192, G.193, L.285, N.286 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: R.17, R.44, T.65 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: E.121, K.131, E.142 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: K.107, D.237, R.320, K.324 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: D.222, F.224, E.225, A.312, K.315 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: R.138, G.140, E.141, E.142 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: K.311, A.312 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: G.155, R.156 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: R.143, E.192, G.193, L.285, N.286 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: R.17, R.44, T.65 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: E.121, K.131, E.142 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: K.107, D.237, R.320, K.324 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: D.222, F.224, E.225, A.312, K.315 Ligand excluded by PLIP

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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, A:N.151 GOL.12: 2 residues within 4Å: Chain A: N.151, F.162 No protein-ligand interaction detected (PLIP) GOL.13: 3 residues within 4Å: Chain A: F.162, L.163, W.167 No protein-ligand interaction detected (PLIP) GOL.14: 2 residues within 4Å: Chain A: Q.223, N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.257 GOL.15: 3 residues within 4Å: Chain A: I.42, P.43, R.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44, A:R.44 GOL.16: 2 residues within 4Å: Chain A: R.120, E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:R.120 GOL.17: 1 residues within 4Å: Chain A: K.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.124, A:K.124 GOL.28: 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, B:N.151 GOL.29: 2 residues within 4Å: Chain B: N.151, F.162 No protein-ligand interaction detected (PLIP) GOL.30: 3 residues within 4Å: Chain B: F.162, L.163, W.167 No protein-ligand interaction detected (PLIP) GOL.31: 2 residues within 4Å: Chain B: Q.223, N.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.257 GOL.32: 3 residues within 4Å: Chain B: I.42, P.43, R.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44, B:R.44 GOL.33: 2 residues within 4Å: Chain B: R.120, E.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.120, B:R.120 GOL.34: 1 residues within 4Å: Chain B: K.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.124, B:K.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corner, T.P. et al., Structure-guided optimisation of N -hydroxythiazole-derived inhibitors of factor inhibiting hypoxia-inducible factor-alpha. Chem Sci (2023)

Release Date

2023-12-13

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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