MolNFT v1 · #113095 · protein

DYRK1A in complex with nitro benzothiazole fragment

5A54 · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A in complex with nitro benzothiazole fragment”. X-ray diffraction, 1 ligand (5PW), 9 pockets (best druggability 0.85). MolNFT v1 #113095 on GenesisL1: 3D structure…

PDB: 5A54
Type: protein
Length: 1,350 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: 5PW
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	342	35% helix, 18% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	340	36% helix, 17% strand	Q13627
C	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	333	37% helix, 15% strand	Q13627
D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	335	35% helix, 19% strand	Q13627

Ligands and binding sites

5PW · N-(6-nitro-1,3-benzothiazol-2-yl)ethanamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

9 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	932	0.85	0.87	100	empty
2	1051	0.82	0.83	85	empty
3	890	0.78	0.81	79	5PW
4	1066	0.78	0.79	89	5PW
5	707	0.78	0.82	86	5PW

Interfaces

6 interfaces between chains.

C–D · 1273 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1243 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 958 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 749 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).

Compared structures

5A54 · DYRK1A in complex with nitro benzothiazole fragment · the same entry in another collection · chain C against C, TM-score 1.00
Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain A 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 5A54 · PDBe 5A54 · UniProt Q13627

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.