SMTL ID : 7o7k.2 (1 other biounit)

Crystal structure of the human DYRK1A kinase domain bound to abemaciclib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Y.195, Q.196, Y.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.196 EDO.5: 5 residues within 4Å: Chain A: C.162, D.163, I.198, Q.199 Ligands: FLC.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.162, A:Q.199 Water bridges: A:Q.199 EDO.6: 6 residues within 4Å: Chain A: P.257, H.259, D.337, D.339, T.342 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.337, A:D.339 EDO.7: 1 residues within 4Å: Chain A: K.356 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: Y.16, R.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.107 Water bridges: A:R.107 EDO.9: 5 residues within 4Å: Chain A: D.18, Y.23, I.24, V.25, Q.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.18, A:V.25, A:V.25 EDO.10: 4 residues within 4Å: Chain A: T.232, E.234, P.310, R.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313, A:R.313 EDO.11: 5 residues within 4Å: Chain A: P.213, Y.214, D.215, P.340, K.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.215 Water bridges: A:E.207, A:D.215 EDO.12: 2 residues within 4Å: Chain A: M.32, R.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.32, A:R.34 EDO.13: 6 residues within 4Å: Chain A: E.84, N.87, L.100, K.101, R.102, H.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87 Water bridges: A:H.103 EDO.14: 5 residues within 4Å: Chain A: R.334, I.344, Y.348, Q.351, H.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.352 EDO.15: 6 residues within 4Å: Chain A: L.253, L.336, D.337, Y.338, D.339 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.337, A:Y.338, A:D.339

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 8 residues within 4Å: Chain A: G.44, S.45, F.46, D.163, K.165, D.183 Ligands: FLC.3, LI.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.45 Water bridges: A:D.163, A:N.168, A:N.168 Salt bridges: A:K.165 FLC.3: 12 residues within 4Å: Chain A: S.45, F.46, K.64, F.72, Q.75, E.79, D.183, G.185, S.186 Ligands: FLC.2, EDO.5, LI.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:Q.75, A:Q.75, A:G.185, A:S.186, A:S.186 Salt bridges: A:K.64

1 x 6ZV: N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine(Non-covalent)

6ZV.4: 18 residues within 4Å: Chain A: I.41, F.46, V.49, A.62, K.64, E.79, V.98, F.114, E.115, M.116, L.117, S.118, N.120, E.167, N.168, L.170, V.182, D.183 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.41, A:F.46, A:V.49, A:F.114, A:L.170 Hydrogen bonds: A:L.117, A:L.117 Salt bridges: A:D.123

1 x LI: LITHIUM ION(Non-functional Binders)

LI.16: 2 residues within 4Å: Ligands: FLC.2, FLC.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaltheuner, I.H. et al., Abemaciclib is a potent inhibitor of DYRK1A and HIP kinases involved in transcriptional regulation. Nat Commun (2021)

Release Date

2021-11-24

Peptides

Dual specificity tyrosine-phosphorylation-regulated kinase 1A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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