SMTL ID : 9hxv.1

Crystal structure of TET2-DNA in complex with IOX1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.261, D.263, H.412 Ligands: 8XQ.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.261, A:D.263, A:D.263, A:H.412

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.12, C.14, H.98, C.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.12, A:C.14, A:H.98, A:C.100 ZN.3: 4 residues within 4Å: Chain A: C.72, C.150, C.152, H.259 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.72, A:C.150, A:C.152, A:H.259 ZN.4: 4 residues within 4Å: Chain A: C.168, C.177, C.237, H.443 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.168, A:C.177, A:C.237, A:H.443

1 x 8XQ: 8-hydroxyquinoline-5-carboxylic acid(Non-covalent)

8XQ.5: 16 residues within 4Å: Chain A: R.140, C.253, A.258, H.261, D.263, T.272, V.274, H.295, E.405, A.407, H.412, T.414, R.427, S.429 Chain B: C.6 Ligands: FE2.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.258, A:V.274, A:T.414 Hydrogen bonds: A:R.140, A:R.140, A:S.429, A:S.429 Salt bridges: A:H.295, A:R.427

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

SO4.6: 4 residues within 4Å: Chain A: H.261, R.262, L.264 Chain C: G.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.262 Salt bridges: A:R.262

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 6 residues within 4Å: Chain A: N.266, S.271, T.272, C.406, A.407, K.408 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Willems, S. et al., Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation. Acs Med.Chem.Lett. (2025)

Release Date

2025-04-09

Peptides

Methylcytosine dioxygenase TET2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methylcytosine dioxygenase TET2