SMTL ID : 8rdz.1 (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: 6 residues within 4Å: Chain A: A.96, E.112, E.115, E.116, E.166 Ligands: MG.3 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.3: 5 residues within 4Å: Chain A: A.96, E.112, 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.6: 5 residues within 4Å: Chain B: A.96, E.112, E.116, E.166 Ligands: MG.8 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.2 MG.8: 5 residues within 4Å: Chain B: A.96, G.97, E.116, E.166 Ligands: MG.6 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.96, B:E.116, H2O.2, H2O.2, H2O.2, H2O.2

2 x 01: Ibrutinib (unbound form)

01.2: 12 residues within 4Å: Chain A: W.28, K.50, R.51, D.60, S.137, N.138, C.139, D.164 Chain B: W.46, E.47, G.135 Ligands: EDO.5 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.28, A:R.51, A:D.60, B:W.46 Hydrogen bonds: A:W.28, B:W.46, B:E.47 pi-Cation interactions: A:W.28, A:W.28 01.7: 12 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, L.98, N.138, C.139 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.51, B:L.98, A:W.46, A:L.136 pi-Cation interactions: B:W.28 Hydrogen bonds: A:W.46, A:E.47, A:G.135

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

EDO.4: 4 residues within 4Å: Chain A: K.175, N.176, L.204 Chain B: A.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.204 EDO.5: 3 residues within 4Å: Chain A: L.98 Chain B: G.135 Ligands: 01.2 No protein-ligand interaction detected (PLIP)

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
A

B
C

ADP-sugar pyrophosphatase

Related Entries With Identical Sequence