SMTL ID : 4tw9.1

Difluoro-dioxolo-benzoimidazol-benzamides as potent inhibitors of CK1delta and epsilon with nanomolar inhibitory activity on cancer cell proliferation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.127, K.154, K.171 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.127, A:K.154, A:K.171 SO4.2: 3 residues within 4Å: Chain A: R.157, R.192, K.263 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.162 Salt bridges: A:R.157, A:R.192 SO4.3: 4 residues within 4Å: Chain A: R.178, Q.214, G.215, I.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215 Salt bridges: A:R.178 SO4.4: 2 residues within 4Å: Chain A: R.274 Ligands: CL.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.270 Salt bridges: A:R.274 SO4.12: 4 residues within 4Å: Chain B: R.127, K.154, K.171, E.189 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.127, B:K.154, B:K.171 SO4.13: 4 residues within 4Å: Chain B: R.157, H.162, R.192, K.263 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.192, B:R.192 Salt bridges: B:R.157, B:H.162, B:R.192 SO4.14: 3 residues within 4Å: Chain B: R.178, Q.214, G.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.215 Water bridges: B:R.178, B:Q.214 Salt bridges: B:R.178 SO4.15: 1 residues within 4Å: Chain B: R.274 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.274

2 x HSJ: octyl beta-L-talopyranoside(Non-covalent)

HSJ.5: 7 residues within 4Å: Chain A: K.14, I.15, S.17, L.25 Chain B: N.94, F.95 Ligands: 386.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.95, A:I.15, A:L.25 Hydrogen bonds: B:N.94, A:K.14, A:K.14 Water bridges: B:N.94 HSJ.11: 7 residues within 4Å: Chain A: N.94, F.95 Chain B: K.14, I.15, G.16, L.25 Ligands: 386.18 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.95, A:F.95, B:I.15, B:L.25 Hydrogen bonds: A:N.94, B:K.14, B:K.14

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: F.260 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: S.267, R.270 Ligands: SO4.4 Ligand excluded by PLIP

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

NA.8: 4 residues within 4Å: Chain A: L.106, D.110, F.273, R.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.110, A:D.110 NA.9: 4 residues within 4Å: Chain A: I.23, K.38, D.149 Ligands: 386.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.18, A:K.38, A:D.149 NA.16: 4 residues within 4Å: Chain B: L.106, D.110, F.273, R.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.110, B:D.110 NA.17: 4 residues within 4Å: Chain B: G.18, I.23, K.38 Ligands: 386.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.18, B:K.38 Water bridges: B:S.19, B:D.149

2 x 386: N-(2,2-difluoro-5H-[1,3]dioxolo[4,5-f]benzimidazol-6-yl)-2-{[2-(trifluoromethoxy)benzoyl]amino}-1,3-thiazole-4-carboxamide(Non-covalent)

386.10: 19 residues within 4Å: Chain A: I.15, I.23, A.36, Y.56, M.80, M.82, E.83, L.84, L.85, G.86, P.87, D.91, L.92, F.95, L.135, I.148, L.293 Ligands: HSJ.5, NA.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.23, A:A.36, A:L.85, A:I.148 Hydrogen bonds: A:L.85, A:L.85, A:L.85, A:D.91 Water bridges: A:S.88, A:D.149 Halogen bonds: A:Y.56 386.18: 19 residues within 4Å: Chain B: I.23, A.36, K.38, Y.56, M.80, M.82, E.83, L.84, L.85, G.86, P.87, D.91, L.92, F.95, L.135, I.148, L.293 Ligands: HSJ.11, NA.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.23, B:A.36, B:L.85, B:D.91, B:I.148 Hydrogen bonds: B:L.85, B:L.85, B:L.85, B:D.91 Water bridges: B:S.88, B:D.149 Halogen bonds: B:Y.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richter, J. et al., Difluoro-dioxolo-benzoimidazol-benzamides As Potent Inhibitors of CK1 delta and epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation. J.Med.Chem. (2014)

Release Date

2014-07-30

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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