SMTL ID : 8c3g.1

Crystal structure of DYRK1A in complex with AZ191

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-tetramer

Ligands

4 x QS0: N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine

QS0.1: 17 residues within 4Å: Chain A: I.41, V.49, A.62, K.64, F.114, E.115, M.116, L.117, S.118, Y.119, N.120, D.123, R.126, L.170, V.182, D.183 Ligands: EDO.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.41, A:A.62, A:F.114, A:L.170, A:V.182 Hydrogen bonds: A:L.117, A:L.117 Salt bridges: A:D.123 QS0.16: 15 residues within 4Å: Chain B: I.41, V.49, A.62, K.64, F.114, E.115, M.116, L.117, S.118, Y.119, N.120, D.123, L.170, V.182, D.183 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.41, B:V.49, B:A.62, B:F.114, B:L.170, B:V.182 Hydrogen bonds: B:L.117, B:L.117 Salt bridges: B:D.123 QS0.23: 15 residues within 4Å: Chain C: I.41, V.49, A.62, K.64, F.114, E.115, M.116, L.117, S.118, N.120, D.123, R.126, L.170, V.182, D.183 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.41, C:A.62, C:F.114, C:L.170, C:V.182 Hydrogen bonds: C:L.117, C:L.117 Water bridges: C:F.184 Salt bridges: C:D.123 QS0.32: 16 residues within 4Å: Chain D: I.41, V.49, A.62, K.64, F.114, E.115, M.116, L.117, S.118, Y.119, N.120, D.123, R.126, L.170, V.182, D.183 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.41, D:V.49, D:A.62, D:F.114, D:L.170, D:V.182 Hydrogen bonds: D:L.117, D:L.117 Salt bridges: D:D.123

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

EDO.2: 7 residues within 4Å: Chain A: L.83, M.86, N.87, K.94, V.98, H.99, L.100 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: K.298, L.299, H.300, K.329 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Q.196, Y.197, V.208, E.242, K.266, K.269 Chain C: N.108 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: T.128, R.131, G.132, R.314 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: I.160, L.190, G.191, Q.192, R.193, Y.214 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: G.191, R.193, P.213, Y.214 Chain B: P.155, S.158, L.190 Ligands: EDO.6, EDO.8 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: P.213, Y.214, D.215, P.340, K.341 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.84, N.87, L.100, K.101, R.102, H.103 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.297, I.302 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.119, D.123, R.126, N.127 Ligands: QS0.1 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: H.99, K.101 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: K.101, R.102 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Y.122, P.166, F.202, Y.203, E.229, P.235 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: Y.195, Q.196, Y.197 Chain C: K.70 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: K.298, L.299, H.300, K.329 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: L.83, M.86, N.87, V.98, H.99, L.100 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: Q.196, Y.197, V.208, L.209, E.242, K.266 Chain D: N.108 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: K.67, F.72 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: K.67 Chain C: N.20, K.67 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: L.83, M.86, N.87, K.94, I.97, V.98, H.99, L.100 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: N.108 Chain C: Q.196, Y.197, V.208, L.209, E.242 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain C: I.160, Q.189, L.190, G.191, Q.192, R.193, Y.214 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: G.191, R.193, P.213, Y.214 Chain D: P.155, S.158, L.190 Ligands: EDO.26 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: E.84, N.87, K.101, R.102, H.103 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain C: K.94, H.99 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: R.334, I.344, Y.348 Ligands: EDO.31 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain C: R.334, T.342, R.343, I.344, Q.345, Y.348 Ligands: EDO.30 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain D: L.83, N.87, V.98, H.99, L.100 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain D: V.252, K.298, L.299, H.300, K.329 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: S.158, L.190 Chain D: L.190, G.191, Q.192, R.193 Ligand excluded by PLIP EDO.36: 1 residues within 4Å: Chain D: R.55 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain D: Y.16, R.107 Ligand excluded by PLIP

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

SO4.21: 3 residues within 4Å: Chain B: K.140, R.176, S.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.177 Salt bridges: B:K.140, B:R.176 SO4.38: 3 residues within 4Å: Chain D: K.140, R.176, S.177 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.177, D:S.177 Salt bridges: D:K.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grygier, P. et al., Structural perspective on the design of selective DYRK1B inhibitors. To Be Published

Release Date

2024-01-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dual specificity tyrosine-phosphorylation-regulated kinase 1A