SMTL ID : 8ptt.1 (1 other biounit)

Human NUDT5 in complex with MRK-952

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x F2V: 6-[(5~{R})-7-[3-chloranyl-4-(trifluoromethyl)phenyl]-2,7-diazaspiro[4.4]nonan-2-yl]-7-methyl-purine(Non-covalent)

F2V.1: 13 residues within 4Å: Chain A: W.28, R.51, G.61, V.62, R.84, A.96, L.98, M.132, I.141, R.196 Chain B: T.45, W.46, E.47 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.46, A:W.28, A:A.96, A:L.98 Hydrogen bonds: B:E.47 pi-Stacking: B:W.46, B:W.46, B:W.46, A:W.28, A:W.28 Halogen bonds: A:V.62, A:R.196 F2V.3: 13 residues within 4Å: Chain A: T.45, W.46, E.47 Chain B: W.28, R.51, G.61, V.62, R.84, A.96, L.98, M.132, I.141, R.196 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.46, B:W.28, B:A.96 Hydrogen bonds: A:E.47 pi-Stacking: A:W.46, A:W.46, A:W.46, B:W.28, B:W.28 Water bridges: B:R.51 Halogen bonds: B:V.62, B:R.196

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: A.96, E.112, E.116, E.166 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.112, A:E.116, A:E.166, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: A.96, E.112, E.116, E.166 Ligands: MG.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.112, B:E.116, B:E.166, H2O.3, H2O.3 MG.5: 1 residues within 4Å: Chain B: H.73 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.73 MG.6: 4 residues within 4Å: Chain B: E.112, E.115, E.166 Ligands: MG.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.112, H2O.3, H2O.3, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Human NUDT5 in complex with MRK-952. To Be Published

Release Date

2024-07-24

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase

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