SMTL ID : 9da3.1

Crystal structure of human DNPH1 bound to inhibitor 2a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x 01: [(3R,4R)-4-hydroxy-1-{[5-(hydroxymethyl)-6-oxo-1,6-dihydropyridin-3-yl]methyl}pyrrolidin-3-yl]methyl dihydrogen phosphate

01.1: 16 residues within 4Å: Chain A: F.8, C.9, G.10, S.11, I.12, R.13, G.14, I.59, D.63, S.81, G.83, V.84, E.87 Chain B: S.111, A.112, M.113 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.59, B:A.112 Hydrogen bonds: A:F.8, A:G.10, A:I.12, A:R.13, A:R.13, A:G.14, A:S.81, A:S.81, A:G.83, A:V.84, B:A.112 Water bridges: A:R.13, A:L.82, A:L.82 Salt bridges: A:D.63, A:E.87 01.2: 16 residues within 4Å: Chain A: S.111, A.112, M.113 Chain B: F.8, C.9, G.10, S.11, I.12, R.13, G.14, I.59, D.63, S.81, G.83, V.84, E.87 20 PLIP interactions: 3 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:A.112, B:I.12, B:I.59 Hydrogen bonds: A:S.111, A:A.112, B:F.8, B:G.10, B:I.12, B:R.13, B:R.13, B:G.14, B:S.81, B:S.81, B:G.83, B:V.84 Water bridges: B:R.13, B:L.82, B:L.82 Salt bridges: B:D.63, B:E.87

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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