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Crystal structure of DYRK1A complexed with KUFAL319 (compound 11)

Analyse Crystal structure of DYRK1A complexed with KUFAL319 (compound 11) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T6A
Type: protein
Length: 1,388 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
EC: 2.7.12.1
UniProt: Q13627
Ligands: MLW, SO4
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	347	35% helix, 18% strand	Q13627

Ligands and binding sites

MLW · 4-chloranyl-5~{H}-cyclohepta[b]indol-10-one · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1158	0.81	0.82	76	SO4
2	334	0.66	0.81	42	MLW
3	328	0.66	0.81	42	PG4, MLW
4	326	0.65	0.80	42	MLW
5	292	0.65	0.81	41	empty

Interfaces

4 interfaces between chains.

A–B · 547 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 436 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 315 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6T6A · Crystal structure of DYRK1A complexed with KuFal319 (compound 11) · the same entry in another collection · chain D against D, TM-score 1.00
Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q13627
Elsewhere: RCSB PDB 6T6A · PDBe 6T6A · UniProt Q13627

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