SMTL ID : 8cg9.1

Crystal structure of human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

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

NI.1: 8 residues within 4Å: Chain A: H.37, H.39, H.42, H.98, D.120 Ligands: XOB.2, R3Z.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.37, A:H.39, A:H.98, A:D.120

1 x XOB: 1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione(Non-covalent)

XOB.2: 12 residues within 4Å: Chain A: D.41, H.42, D.120, T.145, Y.146, G.268, W.269, H.299 Ligands: NI.1, R3Z.3, ZN.4, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.146 Hydrogen bonds: A:D.41, A:Y.146

1 x R3Z: 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

R3Z.3: 13 residues within 4Å: Chain A: H.37, H.39, S.40, D.41, H.42, H.98, D.120, S.185, H.299 Ligands: NI.1, XOB.2, ZN.4, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.40, A:D.41 pi-Cation interactions: A:H.39

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.42, D.120 Ligands: NI.1, XOB.2, R3Z.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:D.120, H2O.2

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 9 residues within 4Å: Chain A: Y.146, K.188, G.268, Y.296, S.297, E.298, H.299 Ligands: XOB.2, R3Z.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.146, A:G.268, A:E.298 Water bridges: A:E.298 Salt bridges: A:K.188, A:H.299

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

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