SMTL ID : 7aya.1 (1 other biounit)

Crystal structure of CK2 bound by compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.77, R.80, R.155, N.189, V.192 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:R.155, A:E.180, A:N.189 Salt bridges: A:K.77, A:R.80, A:R.155 SO4.2: 4 residues within 4Å: Chain A: R.191, V.192, K.198, N.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.238, A:N.238 Salt bridges: A:R.191, A:K.198 SO4.3: 4 residues within 4Å: Chain A: V.31, W.33, K.75, K.102 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.79, A:K.79, A:K.79, A:K.79 Salt bridges: A:K.75, A:K.79, A:K.102 SO4.4: 5 residues within 4Å: Chain A: R.278, K.279, R.280, E.282, R.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.280, A:E.282, A:E.282 Salt bridges: A:R.280, A:R.283 SO4.5: 3 residues within 4Å: Chain A: K.75, K.102, R.107 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.75, A:K.102, A:R.107 SO4.6: 4 residues within 4Å: Chain A: G.48, K.49, Y.50 Ligands: S8W.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.49, A:Y.50 Water bridges: A:D.175

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

EDO.7: 3 residues within 4Å: Chain A: H.276, S.277, K.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.276, A:S.277, A:S.277, A:K.279 EDO.8: 4 residues within 4Å: Chain A: Q.36, Y.39, V.101, A.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:Y.39 EDO.9: 8 residues within 4Å: Chain A: R.8, A.9, R.10, D.210, S.212, H.309, Q.310, R.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:D.210, A:R.312 EDO.10: 3 residues within 4Å: Chain A: D.25, Y.26, E.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25, A:E.27 Water bridges: A:Y.26, A:H.183 EDO.11: 2 residues within 4Å: Chain A: D.299, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.299, A:K.303 EDO.12: 5 residues within 4Å: Chain A: H.160, N.161, M.163, I.174 Ligands: S8W.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161 EDO.13: 5 residues within 4Å: Chain A: P.6, S.7, R.8, G.185, M.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.7, A:R.8 EDO.14: 4 residues within 4Å: Chain A: V.11, Y.12, T.314, R.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.12, A:T.314, A:T.314 Water bridges: A:D.145, A:E.317 EDO.15: 4 residues within 4Å: Chain A: R.280, W.281, L.298, D.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.281 Water bridges: A:D.299 EDO.16: 4 residues within 4Å: Chain A: D.130, Y.131, R.134, T.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.326 Water bridges: A:Y.131 EDO.17: 5 residues within 4Å: Chain A: V.73, K.77, I.78, E.81, G.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.77 Water bridges: A:K.68 EDO.18: 6 residues within 4Å: Chain A: V.248, L.249, R.278, K.279, W.281, D.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.278

1 x S8W: ~{N}-[2-[(1~{R},2~{R})-2-(aminomethyl)cyclopropyl]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide(Non-covalent)

S8W.19: 17 residues within 4Å: Chain A: R.47, G.48, S.51, V.53, V.66, K.68, I.95, F.113, E.114, H.115, V.116, N.118, M.163, I.174, D.175 Ligands: SO4.6, EDO.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.53, A:V.53, A:V.66, A:K.68, A:N.118, A:I.174 Hydrogen bonds: A:V.116, A:D.175 Water bridges: A:K.158, A:K.158

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
A

Casein kinase II subunit alpha

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