SMTL ID : 7ay9.2 (2 other biounits)

Crystal structure of CK2 bound by compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.77, R.80, R.155, N.189 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:R.155, A:R.155 Salt bridges: A:K.77, A:R.80, A:R.155 SO4.2: 4 residues within 4Å: Chain A: K.229, H.234, R.244 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.234 Water bridges: A:K.229, A:H.234 Salt bridges: A:K.229, A:R.244 SO4.3: 4 residues within 4Å: Chain A: W.33, K.75, K.102 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.79, A:K.79 Salt bridges: A:K.75, A:K.102 SO4.4: 3 residues within 4Å: Chain A: K.75, K.102 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.75, A:K.102 SO4.5: 7 residues within 4Å: Chain A: H.29, V.30, V.31, E.32, I.82, E.86, I.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.32, A:E.86 Salt bridges: A:H.29

1 x S92: 7-(cyclopropylamino)-5-(5-(6-oxo-1,6-dihydropyridin-3-yl)-1-(2-(piperidin-1-yl)ethyl)-1H-1,2,3-triazol-4-yl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

S92.6: 18 residues within 4Å: Chain A: L.45, G.46, R.47, V.53, V.66, K.68, I.95, F.113, E.114, H.115, V.116, N.118, H.160, M.163, I.174, D.175 Ligands: EDO.11, EDO.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.53, A:V.53, A:V.66, A:I.174 Hydrogen bonds: A:V.116, A:V.116, A:D.175 Water bridges: A:W.176

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

EDO.7: 1 residues within 4Å: Chain A: K.44 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: R.191, V.192, K.198, N.238 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.191, A:K.198, A:N.238, A:N.238 EDO.9: 3 residues within 4Å: Chain A: E.252, S.277, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.278, A:R.278 Water bridges: A:E.252 EDO.10: 7 residues within 4Å: Chain A: K.229, F.232, F.233, R.244, V.248, F.284 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.244 Water bridges: A:K.229, A:H.234 EDO.11: 3 residues within 4Å: Chain A: G.46, R.47 Ligands: S92.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.47 EDO.12: 5 residues within 4Å: Chain A: Q.36, Y.39, V.67, D.103, P.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.36, A:Y.39, A:D.103 Water bridges: A:L.41 EDO.13: 4 residues within 4Å: Chain A: S.277, R.278, K.279, R.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.277, A:R.278, A:R.280, A:R.280 EDO.14: 4 residues within 4Å: Chain A: S.194, R.195, N.238 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195, A:R.195 EDO.15: 3 residues within 4Å: Chain A: H.276, S.277, K.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.277, A:K.279 EDO.16: 2 residues within 4Å: Chain A: P.322, Y.325 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain A: Y.196, H.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.196 EDO.18: 4 residues within 4Å: Chain A: Y.131, D.132, F.135, R.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.132, A:R.169 EDO.19: 3 residues within 4Å: Chain A: H.160, M.163 Ligands: S92.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Date, M., Metadynamics simulations of CK2 compound unbinding to understand slow dissociation kinetics. To Be Published

Release Date

2021-11-24

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Casein kinase II subunit alpha

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