SMTL ID : 9da6.1

Crystal structure of human DNPH1 bound to inhibitor 3a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x NR1: (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium(Non-covalent)

NR1.1: 18 residues within 4Å: Chain A: Y.7, F.8, C.9, G.10, S.11, I.12, R.13, G.14, E.38, H.39, D.63, S.81, L.82, G.83, V.84, E.87 Chain B: S.111, M.113 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.8, A:G.10, A:I.12, A:R.13, A:G.14, A:D.63, A:S.81, A:L.82, A:G.83, A:V.84, A:E.87, B:S.111 Water bridges: A:S.81 NR1.3: 18 residues within 4Å: Chain A: S.111, M.113 Chain B: Y.7, F.8, C.9, G.10, S.11, I.12, R.13, G.14, E.38, H.39, D.63, S.81, L.82, G.83, V.84, E.87 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.84 Hydrogen bonds: B:G.10, B:I.12, B:R.13, B:G.14, B:H.39, B:S.81, B:L.82, B:G.83, B:V.84, B:E.87, A:S.111, A:S.111 Water bridges: B:S.81

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

EDO.2: 3 residues within 4Å: Chain A: M.2, P.4, F.32 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, A.G. et al., Transition State Analogs of Human DNPH1 Reveal Two Electrophile Migration Mechanisms. J.Med.Chem. (2025)

Release Date

2025-02-05

Peptides

5-hydroxymethyl-dUMP N-hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5-hydroxymethyl-dUMP N-hydrolase

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