SMTL ID : 5n1v.2 (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

2 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:R.155, A:N.189 Salt bridges: A:K.77, A:R.80, A:R.155 SO4.2: 3 residues within 4Å: Chain A: W.33, K.75, K.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.33 Salt bridges: A:K.75, A:K.102

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

EDO.3: 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.4: 3 residues within 4Å: Chain A: R.280, W.281, E.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.282, A:E.282 EDO.5: 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.6: 5 residues within 4Å: Chain A: R.191, V.192, A.193, K.198, N.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.191, A:A.193, A:K.198, A:N.238 EDO.7: 10 residues within 4Å: Chain A: R.8, A.9, R.10, V.11, D.210, Y.211, S.212, H.309, Q.310 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10, A:S.212 EDO.8: 3 residues within 4Å: Chain A: Q.36, D.103, A.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:T.108 EDO.9: 8 residues within 4Å: Chain A: V.11, H.148, Y.211, S.212, M.215, T.314, A.315 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:Y.12, A:D.145 EDO.10: 2 residues within 4Å: Chain A: K.229, R.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.229, A:K.229, A:R.244, A:R.244 EDO.11: 3 residues within 4Å: Chain A: K.75, K.102, R.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.75, A:K.102, A:R.107

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

8GQ.12: 13 residues within 4Å: Chain A: L.45, V.53, V.66, I.95, F.113, E.114, V.116, N.117, N.118, H.160, M.163, I.174, D.175 8 PLIP interactions: 8 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 Water bridges: 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
B

Casein kinase II subunit alpha

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