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

Crystal structure of the human DYRK1A kinase domain bound to abemaciclib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 8 residues within 4Å: Chain A: G.44, S.45, F.46, D.163, K.165, D.183 Ligands: FLC.2, LI.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.45 Water bridges: A:K.43, A:N.168, A:N.168 Salt bridges: A:K.165 FLC.2: 11 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.1, LI.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:Q.75, A:Q.75, A:G.185, A:S.186 Water bridges: A:K.64, A:E.79 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.3: 18 residues within 4Å: Chain A: I.41, F.46, A.62, K.64, E.79, V.98, F.114, E.115, M.116, L.117, S.118, N.120, D.123, E.167, N.168, L.170, V.182, D.183 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.46, A:F.114, A:L.170, A:V.182 Hydrogen bonds: A:L.117, A:L.117 Salt bridges: A:D.123

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

EDO.4: 4 residues within 4Å: Chain A: G.132, V.133, S.134, R.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:R.314, A:R.314 EDO.5: 3 residues within 4Å: Chain A: E.36, Y.53, R.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.55 Water bridges: A:Y.53 EDO.6: 5 residues within 4Å: Chain A: P.213, Y.214, D.215, P.340, K.341 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.214 EDO.7: 4 residues within 4Å: Chain A: S.200, R.201, F.202, Y.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.202 EDO.8: 5 residues within 4Å: Chain A: P.155, E.156, S.158, Q.189, L.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.190 EDO.9: 3 residues within 4Å: Chain A: D.19, N.20, Y.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.21, A:Y.21 EDO.10: 5 residues within 4Å: Chain A: N.13, D.14, Y.16, R.107, N.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.14, A:R.107 Water bridges: A:N.108, A:N.108, A:N.108 EDO.12: 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

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 5 residues within 4Å: Chain A: I.255, P.256, P.257, A.258, H.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.255, A:A.258, A:H.259, A:H.259

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

LI.13: 2 residues within 4Å: Ligands: FLC.1, FLC.2 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
A

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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