SMTL ID : 9da2.1

Crystal structure of human DNPH1 bound to inhibitor 1b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

2 x 01: 1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

01.1: 18 residues within 4Å: Chain A: Y.7, F.8, C.9, G.10, S.11, I.12, R.13, G.14, I.59, D.63, S.81, L.82, G.83, V.84, E.87 Chain B: S.111, A.112, M.113 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.10, A:I.12, A:R.13, A:G.14, A:S.81, A:L.82, A:G.83, A:V.84, A:E.87, B:S.111, B:S.111, B:A.112 Water bridges: A:Y.7 Hydrophobic interactions: B:A.112 01.5: 20 residues within 4Å: Chain A: S.111, A.112, M.113 Chain B: Y.7, F.8, C.9, G.10, S.11, I.12, R.13, G.14, I.59, D.63, S.81, L.82, G.83, V.84, E.87 Ligands: EDO.8, PEG.10 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.12, A:A.112 Hydrogen bonds: B:G.10, B:I.12, B:R.13, B:G.14, B:S.81, B:S.81, B:L.82, B:G.83, B:V.84, B:E.87, A:S.111, A:A.112 Water bridges: B:Y.7

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

EDO.2: 5 residues within 4Å: Chain A: T.78, R.103, Q.105, S.106, E.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.103, A:R.103 Water bridges: A:E.130 EDO.3: 4 residues within 4Å: Chain A: R.28, R.31, E.134, D.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.28 Water bridges: A:R.28, A:R.28, A:R.31 EDO.4: 1 residues within 4Å: Chain A: Q.105 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain B: G.107, R.108, V.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.107 Water bridges: B:V.109 EDO.7: 5 residues within 4Å: Chain B: R.16, R.19, E.23 Ligands: EDO.8, PEG.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.19, B:R.19 Water bridges: B:E.23 EDO.8: 4 residues within 4Å: Chain B: I.12 Ligands: 01.5, EDO.7, PEG.10 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: A.118, D.119 Chain B: R.57 No protein-ligand interaction detected (PLIP)

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

PEG.10: 10 residues within 4Å: Chain B: F.8, G.10, S.11, I.12, R.16, R.19, Y.22 Ligands: 01.5, EDO.7, EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.16, B:R.16

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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