SMTL ID : 8cew.1

Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 2 residues within 4Å: Chain A: L.193, I.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.190

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 8 residues within 4Å: Chain A: H.37, H.39, H.42, H.98, D.120 Ligands: ZN.3, UFI.4, UFI.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.37, A:H.39, A:H.98, A:D.120

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.42, D.120 Ligands: NI.2, UFI.4, UFI.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:D.120, H2O.2

2 x UFI: 6-methoxy-2-oxidanyl-benzo[de]isoquinoline-1,3-dione(Non-covalent)

UFI.4: 12 residues within 4Å: Chain A: H.37, H.39, S.40, D.41, H.42, H.98, D.120, Y.184, H.299 Ligands: NI.2, ZN.3, UFI.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.184 Hydrogen bonds: A:D.41 pi-Stacking: A:H.39 UFI.5: 7 residues within 4Å: Chain A: D.41, H.42, D.120, H.299 Ligands: NI.2, ZN.3, UFI.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.41 Hydrogen bonds: A:D.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bielinski, M. et al., Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target. Chem Sci (2024)

Release Date

2024-02-21

Peptides

DNA cross-link repair 1A protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA cross-link repair 1A protein

Related Entries With Identical Sequence