SMTL ID : 8rdz.2 (1 other biounit)

Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with Ibrutinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: A.96, E.112, E.116, E.166 Ligands: MG.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.112, A:E.166, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain A: A.96, E.116, E.166 Ligands: MG.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.96, A:E.116, H2O.1, H2O.1, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain B: A.96, E.112, E.116, E.166 Ligands: MG.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.112, B:E.116, B:E.166, H2O.2, H2O.3 MG.11: 5 residues within 4Å: Chain B: A.96, E.112, E.116, E.166 Ligands: MG.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.96, B:E.116, H2O.2, H2O.2, H2O.3

2 x 01: Ibrutinib (unbound form)

01.2: 13 residues within 4Å: Chain A: W.28, V.49, K.50, R.51, D.60, S.137, N.138, C.139 Chain B: W.46, E.47, G.135, L.136 Ligands: EDO.5 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:R.51, B:L.136 Hydrogen bonds: B:E.47, B:E.47 pi-Stacking: B:W.46, B:W.46 01.7: 13 residues within 4Å: Chain A: W.46, E.47, G.135, L.136 Chain B: W.28, V.29, K.50, R.51, D.60, S.137, N.138, C.139 Ligands: EDO.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.28, B:V.29, A:W.46, A:L.136 Hydrogen bonds: B:W.28, A:W.46, A:E.47

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

EDO.3: 4 residues within 4Å: Chain A: V.67, T.145, K.175 Chain B: H.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.175 EDO.4: 5 residues within 4Å: Chain A: Q.69, R.70, T.71, N.149, D.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 EDO.5: 3 residues within 4Å: Chain A: R.84 Chain B: W.46 Ligands: 01.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.84, A:R.84 Water bridges: A:Q.82, A:A.96, A:A.96 EDO.8: 4 residues within 4Å: Chain A: W.46 Chain B: R.84, L.98 Ligands: 01.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.84 Water bridges: B:R.84 EDO.9: 6 residues within 4Å: Chain B: V.62, A.96, G.97, L.98, C.139, I.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.62, B:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balikci, E. et al., Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J.Med.Chem. (2024)

Release Date

2024-05-01

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

ADP-sugar pyrophosphatase

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