SMTL ID : 8r8e.2 (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 1PE: PENTAETHYLENE GLYCOL

1PE.1: 5 residues within 4Å: Chain A: D.38, S.39, 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

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

YOX.2: 12 residues within 4Å: Chain A: K.43, V.49, A.62, K.64, V.98, F.114, E.115, 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:V.182, A:V.182 Hydrogen bonds: A:D.183 Water bridges: A:F.184 Halogen bonds: A:L.117

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

EPE.3: 3 residues within 4Å: Chain A: K.266, R.268, K.269 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.266, A:K.269 EPE.5: 7 residues within 4Å: Chain A: L.124, L.137, K.140, P.174, K.175, 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

3 x GOL: GLYCEROL

GOL.4: 2 residues within 4Å: Chain A: K.69, K.70 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: D.262, Q.263, A.264, P.265 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.265 GOL.9: 6 residues within 4Å: Chain A: K.341, T.342, R.343, I.344, Q.345, Y.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.341, A:Q.345, A:Q.345 Water bridges: A:Q.345

3 x EDO: 1,2-ETHANEDIOL

EDO.6: 6 residues within 4Å: Chain A: I.255, P.256, P.257, A.258, T.278, W.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.256, A:W.279 Water bridges: A:A.258 EDO.8: 5 residues within 4Å: Chain A: R.334, D.337, T.342, R.343, I.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.334, A:D.337, A:I.344 EDO.11: 9 residues within 4Å: Chain A: G.304, V.305, E.306, T.307, G.308, R.314, H.320, V.322, Y.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.304, A:G.308, A:R.314

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.10: 8 residues within 4Å: Chain A: R.193, I.194, Y.195, Q.196, G.211, M.212, P.213, Y.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.193, A:R.193

5 x SO4: SULFATE ION

SO4.12: 3 residues within 4Å: Chain A: R.131, 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 SO4.13: 4 residues within 4Å: Chain A: N.241, E.242, V.243, K.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.242, A:V.243 Water bridges: A:K.269 Salt bridges: A:K.269 SO4.14: 5 residues within 4Å: Chain A: K.298, L.299, H.300, K.329, L.333 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.299, A:H.300 Water bridges: A:K.329, A:K.329 Salt bridges: A:K.298, A:K.329 SO4.15: 3 residues within 4Å: Chain A: S.134, N.136, L.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.134, A:N.136, A:L.137 Water bridges: A:N.136 SO4.16: 2 residues within 4Å: Chain A: K.101, R.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.34 Water bridges: A:R.34, A:R.102 Salt bridges: A:R.102

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
B

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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