SMTL ID : 9hph.1 (1 other biounit)

Protein kinase CK2 bound to KDX1381

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: W.55, K.101, K.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.55 Salt bridges: A:K.101, A:K.124 SO4.2: 3 residues within 4Å: Chain A: R.213, K.220, N.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.215, A:N.260 Salt bridges: A:K.71, A:K.220 SO4.3: 4 residues within 4Å: Chain A: K.99, R.102, R.177, N.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.211 Water bridges: A:R.177, A:R.177 Salt bridges: A:K.99, A:R.102, A:R.177 SO4.7: 4 residues within 4Å: Chain A: R.300, K.301, R.302, R.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.302 Salt bridges: A:R.302, A:R.305 SO4.8: 4 residues within 4Å: Chain A: Y.147, P.181, H.182 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.147 Water bridges: A:H.182, A:H.182 Salt bridges: A:H.182 SO4.9: 3 residues within 4Å: Chain A: G.112, G.113, Y.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.168 SO4.10: 6 residues within 4Å: Chain A: G.112, G.113, P.114, N.115, I.116, R.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.115, A:I.116, A:T.118 Water bridges: A:G.113 Salt bridges: A:R.194 SO4.11: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.266, A:K.269 SO4.12: 4 residues within 4Å: Chain A: V.315, S.316, P.317, L.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.316 SO4.13: 4 residues within 4Å: Chain A: R.32, Q.332, S.333, E.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.333 Water bridges: A:L.335 Salt bridges: A:R.32

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: R.297, H.298, S.299, K.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.299, A:K.301 PEG.5: 2 residues within 4Å: Chain A: D.321, K.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.325

1 x 01: ~{N}-[2-[4-[[4-(2-ethanoyl-5-fluoranyl-1~{H}-indol-3-yl)-1,2,3-triazol-1-yl]methyl]piperidin-1-yl]ethyl]-4-(2-fluoranyl-6-oxidanyl-phenyl)benzenesulfonamide

01.6: 30 residues within 4Å: Chain A: L.67, G.68, V.75, V.88, K.90, I.117, F.135, E.136, H.137, V.138, N.140, F.143, L.146, Y.147, L.150, I.155, Y.158, M.159, P.181, H.182, V.184, M.185, I.186, I.196, D.197, M.243, L.244, M.247 Ligands: SO4.8, CL.14 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.75, A:V.88, A:V.88, A:I.117, A:F.135, A:F.135, A:L.150, A:V.184, A:I.186, A:I.196, A:M.243, A:M.247 Hydrogen bonds: A:N.140, A:V.184, A:I.186 Halogen bonds: A:V.138

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

CL.14: 4 residues within 4Å: Chain A: K.90, F.135, D.197 Ligands: 01.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marlhoux, L. et al., Discovery of KDX1381, a Bivalent CK2 alpha Inhibitor for the Treatment of Solid Tumors as a Single Agent or in Combination. J.Med.Chem. (2025)

Release Date

2025-07-30

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Casein kinase II subunit alpha

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