SMTL ID : 5n1v.1 (1 other biounit)

Crystal structure of the protein kinase CK2 catalytic subunit in complex with pyrazolo-pyrimidine macrocyclic ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 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: 3 residues within 4Å: Chain A: R.191, K.198, N.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.238 Salt bridges: A:R.191, A:K.198 SO4.3: 4 residues within 4Å: Chain A: W.33, K.75, K.102 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.33 Salt bridges: A:K.75, A:K.79, A:K.102 SO4.4: 4 residues within 4Å: Chain A: K.279, R.280, E.282, R.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.280 Salt bridges: A:R.280, A:R.283 SO4.5: 4 residues within 4Å: Chain A: K.75, K.102, R.107 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.75, A:K.102, A:R.107

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

EDO.6: 4 residues within 4Å: Chain A: Q.36, I.69, V.101, A.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 EDO.7: 4 residues within 4Å: Chain A: W.24, D.25, Y.26, E.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.25, A:E.27 EDO.8: 2 residues within 4Å: Chain A: D.299, K.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.303 EDO.9: 9 residues within 4Å: Chain A: R.8, A.9, R.10, D.210, S.212, H.309, Q.310, R.312 Ligands: EDO.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:D.210, A:S.212, A:Q.310, A:R.312, A:R.312 Water bridges: A:S.212 EDO.10: 8 residues within 4Å: Chain A: V.11, H.148, Y.211, S.212, M.215, T.314, A.315 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:S.212, A:T.314, A:R.316 EDO.11: 1 residues within 4Å: Chain A: K.75 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: H.276, S.277, K.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.277, A:S.277, A:K.279

1 x 8GQ: pyrazolo-pyrimidine macrocycle(Non-covalent)

8GQ.13: 14 residues within 4Å: Chain A: L.45, V.53, V.66, I.95, F.113, E.114, H.115, V.116, N.117, N.118, H.160, M.163, I.174, D.175 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.53, A:V.66, A:N.118 Hydrogen bonds: A:V.116, A:V.116, A:N.118, A:D.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCoull, W. et al., Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. J. Med. Chem. (2017)

Release Date

2017-05-17

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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