SMTL ID : 9mft.1

Human DHX9 in Complex with ATX968 and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x 01: (4M)-N-[3-chloro-5-(methanesulfonamido)phenyl]-4-(3-methylpyridin-2-yl)thiophene-2-carboxamide

01.1: 15 residues within 4Å: Chain A: P.193, W.194, T.195, S.324, S.329, L.331, M.339, C.341, V.345, L.346, K.349, G.353, I.354, R.355, I.357 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.331, A:L.331 Hydrogen bonds: A:P.193, A:W.194, A:S.324, A:R.355 pi-Stacking: A:W.194 pi-Cation interactions: A:K.349 Halogen bonds: A:C.341

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: L.240, T.265, G.266, C.267, G.268, K.269, T.270, T.271, R.308, F.551, T.573, N.575 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:T.270, A:T.271, A:T.573, A:N.575 Water bridges: A:K.269, A:K.269, A:T.270, A:D.363 Salt bridges: A:K.269 pi-Stacking: A:F.551 pi-Cation interactions: A:R.308, A:R.308

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.270, E.364, T.570 Ligands: ADP.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.270, A:E.364, H2O.1, H2O.1, H2O.1

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

EDO.4: 1 residues within 4Å: Chain A: R.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.299 Water bridges: A:P.297, A:I.300 EDO.5: 3 residues within 4Å: Chain A: H.527, H.531, R.532 No protein-ligand interaction detected (PLIP)

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

SO4.6: 5 residues within 4Å: Chain A: R.326, T.342, G.344, V.345, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.326, A:G.344, A:V.345 Water bridges: A:R.326 Salt bridges: A:R.348 SO4.7: 3 residues within 4Å: Chain A: H.539, S.540, T.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.540, A:S.540 SO4.8: 5 residues within 4Å: Chain A: G.664, I.665, G.666, Q.667, E.685 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.665, A:G.666, A:Q.667, A:E.685 SO4.9: 5 residues within 4Å: Chain A: P.836, D.841, R.992, P.993, S.994 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.841, A:S.994 Salt bridges: A:R.992

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daniels, M.H. et al., Discovery of ATX968: An Orally Available Allosteric Inhibitor of DHX9. J.Med.Chem. (2025)

Release Date

2025-05-07

Peptides

ATP-dependent RNA helicase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase A

Related Entries With Identical Sequence