SMTL ID : 6rch.1

Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.180, Q.216, G.217, K.226 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.217 Water bridges: A:R.180, A:R.180, A:R.180, A:G.217, A:L.218, A:K.226, A:K.226, A:K.226 Salt bridges: A:R.180, A:K.226 SO4.2: 4 residues within 4Å: Chain A: R.129, K.156, E.191 Ligands: EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.191 Water bridges: A:R.129, A:R.129, A:R.129 Salt bridges: A:R.129, A:K.156 SO4.3: 3 residues within 4Å: Chain A: R.159, R.194, K.265 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.263 Water bridges: A:R.159, A:R.159, A:H.164, A:R.194, A:K.265 Salt bridges: A:R.159, A:R.194, A:K.265 SO4.11: 4 residues within 4Å: Chain B: R.180, Q.216, G.217, K.226 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.217 Water bridges: B:Q.216, B:L.218, B:K.226, B:K.226, B:K.226 Salt bridges: B:R.180, B:K.226 SO4.12: 4 residues within 4Å: Chain B: R.129, K.156, K.173, E.191 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.129 Salt bridges: B:R.129, B:K.156, B:R.170, B:K.173 SO4.13: 4 residues within 4Å: Chain B: S.123, R.159, H.164, K.265 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.159 Salt bridges: B:R.159, B:H.164, B:K.265 SO4.14: 3 residues within 4Å: Chain B: S.269, R.272, R.276 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.272 Salt bridges: B:R.272, B:R.276

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

EDO.4: 5 residues within 4Å: Chain A: F.102, S.103, L.104, N.209, Y.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.102 Water bridges: A:Y.246 EDO.5: 4 residues within 4Å: Chain A: D.112, R.276, F.279, Y.286 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.108 EDO.6: 4 residues within 4Å: Chain A: K.173, N.174, T.176 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174, A:N.174 EDO.7: 1 residues within 4Å: Chain A: Y.169 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: R.170, K.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:K.173 Water bridges: A:R.170 EDO.15: 7 residues within 4Å: Chain B: E.35, T.69, I.70, R.71, V.83, M.84, E.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.35, B:I.70, B:R.71

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: D.196, D.197, S.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.192, A:S.200 NA.16: 4 residues within 4Å: Chain B: N.145, Y.288, F.290, N.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.145, B:N.145, B:N.293

1 x K0B: ~{N}-[[4,5-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-naphthalen-2-yl-purin-6-amine(Non-covalent)

K0B.10: 20 residues within 4Å: Chain A: R.15, I.17, G.18, S.19, I.25, L.27, A.38, K.40, E.54, Y.58, P.68, M.82, M.84, E.85, L.86, L.87, G.88, L.137, I.150, D.151 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.25, A:K.40, A:Y.58, A:P.68, A:M.84, A:I.150, A:I.150, A:D.151 Hydrogen bonds: A:L.87, A:L.87, A:D.93 Water bridges: A:S.19, A:S.90 Halogen bonds: A:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor. To Be Published

Release Date

2020-03-25

Peptides

Casein kinase I isoform delta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Casein kinase I isoform delta

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