SMTL ID : 8r8e.4 (3 other biounits)

DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

1 x YOX: 2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile

YOX.1: 14 residues within 4Å: Chain A: K.43, F.46, V.49, A.62, K.64, V.98, F.114, E.115, M.116, L.117, N.168, L.170, V.182, D.183 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.49, A:A.62, A:V.98, A:F.114, A:F.114, A:L.117, A:V.182, A:V.182, A:V.182 Hydrogen bonds: A:D.183

2 x GOL: GLYCEROL

GOL.2: 5 residues within 4Å: Chain A: P.155, E.156, S.158, Q.189, L.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.155, A:Q.189 GOL.4: 5 residues within 4Å: Chain A: T.342, R.343, I.344, Q.345, Y.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.345, A:Q.345

1 x 1PE: PENTAETHYLENE GLYCOL

1PE.3: 5 residues within 4Å: Chain A: D.38, I.41, K.51, W.60, M.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.39, A:S.39, A:K.51

7 x SO4: SULFATE ION

SO4.5: 3 residues within 4Å: Chain A: K.140, R.176, S.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.177, A:S.177 Salt bridges: A:K.140, A:R.176 SO4.6: 4 residues within 4Å: Chain A: N.241, E.242, V.243, K.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.242, A:V.243 Water bridges: A:K.269, A:K.269 Salt bridges: A:K.269 SO4.7: 5 residues within 4Å: Chain A: R.131, G.132, V.133, S.134, R.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.132, A:S.134 Salt bridges: A:R.131, A:R.314 SO4.8: 2 residues within 4Å: Chain A: S.134, N.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:N.136 SO4.9: 1 residues within 4Å: Chain A: R.176 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.176 SO4.10: 4 residues within 4Å: Chain A: R.34, E.57, K.101, R.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34 Salt bridges: A:R.102 SO4.11: 2 residues within 4Å: Chain A: R.131, R.313 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.131, A:R.313

1 x PO4: PHOSPHATE ION

PO4.12: 2 residues within 4Å: Chain A: R.201, R.204 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.201, A:R.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engelhardt, M.U. et al., Halogen Bonding on Water─A Drop in the Ocean?. J Chem Theory Comput (2024)

Release Date

2024-09-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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