SMTL ID : 9dex.1

Crystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: K.6, I.7, I.141 Chain B: G.116, L.118, F.126 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: F.47, T.48, F.49, W.86, G.94 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: K.15, S.105, D.106, P.107, K.108, R.109, T.110 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: A.62, F.65, K.66, S.70, Q.71, V.72 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: Q.160 Ligands: PEG.10, IY4.24 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: K.92 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: A.11, N.13, L.30, S.31, K.34, G.136 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: F.49 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: A.5, Y.115, G.116, I.141 Chain B: I.141 Ligands: EDO.14, EDO.22 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: G.116, L.118, F.126 Chain B: K.6, I.7, I.141 Ligands: EDO.12 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: K.15, T.17, D.27 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: K.15, S.105, D.106, P.107, K.108, T.110 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: A.62, K.66, S.70, Q.71, V.72 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: K.108, R.109, T.110, Q.113 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: A.11, N.13, L.30, S.31, K.34, G.136 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: A.5, Y.115, G.116, I.141 Ligands: EDO.12 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: P.21, N.100 Ligand excluded by PLIP

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

SO4.3: 4 residues within 4Å: Chain A: R.61, S.151, V.152, D.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.152, A:D.153 Water bridges: A:R.61, A:R.61 Salt bridges: A:R.61 SO4.5: 7 residues within 4Å: Chain A: L.118, K.119, A.120, D.121 Chain B: K.6, I.7, H.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.7, A:A.120, A:D.121 Salt bridges: B:K.6, B:H.9 SO4.15: 4 residues within 4Å: Chain B: R.61, S.151, V.152, D.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.61, B:S.151, B:V.152, B:D.153 SO4.19: 5 residues within 4Å: Chain A: H.9 Chain B: L.118, K.119, A.120, D.121 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:H.9, A:H.9, B:K.119, B:D.121 Salt bridges: A:H.9 Hydrogen bonds: B:A.120, B:D.121

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 6 residues within 4Å: Chain A: D.153, L.156, R.157, Q.160 Ligands: EDO.7, IY4.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.157 Water bridges: A:Q.160 PEG.13: 4 residues within 4Å: Chain A: T.17, F.25, D.27, H.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.25 Water bridges: A:D.27

1 x IY4: methyl N-(2-{[(2M)-2-(pyridin-3-yl)-1,3-thiazole-4-carbonyl]amino}prop-2-enoyl)-D-alaninate(Covalent)

IY4.24: 10 residues within 4Å: Chain A: R.157, Q.160, A.161, F.164, T.165 Chain B: C.51, G.149, R.150 Ligands: EDO.7, PEG.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.157, A:T.165 Water bridges: A:R.157, A:R.157 Salt bridges: A:R.157 Hydrogen bonds: B:G.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lowther, W.T. et al., Crystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097. To Be Published

Release Date

2025-10-29

Peptides

Peroxiredoxin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxiredoxin-1