SMTL ID : 7z5n.1 (7 other biounits)

Crystal structure of DYRK1A in complex with CX-4945

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

monomer

Ligands

1 x 3NG: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid(Non-covalent)

3NG.1: 16 residues within 4Å: Chain A: I.40, G.41, K.42, G.43, F.45, V.48, A.61, K.63, F.113, E.114, M.115, L.116, L.169, V.181, D.182 Ligands: SO4.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.40, A:I.40, A:V.48, A:A.61, A:F.113, A:F.113, A:L.169, A:V.181, A:V.181 Hydrogen bonds: A:L.116, A:D.182 Water bridges: A:F.183, A:F.183 Salt bridges: A:K.63

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

SO4.2: 5 residues within 4Å: Chain A: N.240, E.241, V.242, K.268 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.241, A:V.242 Salt bridges: A:K.268 SO4.3: 3 residues within 4Å: Chain A: V.132, S.133, R.313 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.133, A:S.133 Water bridges: A:S.133, A:S.133 Salt bridges: A:R.313 SO4.4: 5 residues within 4Å: Chain A: G.43, S.44, K.164, D.182 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.44 Water bridges: A:S.44, A:K.164 Salt bridges: A:K.164 SO4.5: 6 residues within 4Å: Chain A: F.45, E.166, N.167, D.182 Ligands: 3NG.1, SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.167 SO4.6: 3 residues within 4Å: Chain A: K.265, K.268 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.265, A:K.268

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 6 residues within 4Å: Chain A: L.72, Q.76, V.79, H.102, M.104, L.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.76 PG4.8: 5 residues within 4Å: Chain A: D.37, S.38, K.50, W.59, M.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50

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

PEG.9: 4 residues within 4Å: Chain A: F.71, Q.74, S.185, Y.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.194

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

EDO.10: 3 residues within 4Å: Chain A: K.297, H.299, K.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.299 EDO.11: 2 residues within 4Å: Chain A: P.154, S.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.154 EDO.12: 2 residues within 4Å: Chain A: K.68, K.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.69 Water bridges: A:N.67, A:N.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grygier, P. et al., Crystal structure DYRK1A in complex with CX-4945. To Be Published

Release Date

2023-03-22

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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