Research workbench

IRAK4-inhibitor co-structure

Analyse IRAK4-inhibitor co-structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YP8
Type: protein
Length: 1,146 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-1 receptor-associated kinase 4
EC: 2.7.11.1
UniProt: Q9NWZ3
Ligands: 4GF
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	287	41% helix, 17% strand	Q9NWZ3
B	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	281	38% helix, 16% strand	Q9NWZ3
C	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	290	42% helix, 18% strand	Q9NWZ3
D	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	288	42% helix, 18% strand	Q9NWZ3

Ligands and binding sites

4GF · N-{1-(4-cyclopropyl-2-fluorophenyl)-3-[1-(propan-2-yl)piperidin-4-yl]-1H-pyrazol-5-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	758	0.87	0.90	109	empty
2	217	0.74	0.89	41	4GF
3	281	0.73	0.86	43	4GF
4	684	0.72	0.79	55	empty
5	825	0.72	0.77	57	empty

Interfaces

5 interfaces between chains.

A–D · 677 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 624 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 581 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 526 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 483 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (phosphorylation).

Compared structures

4YP8 · Irak4-inhibitor co-structure · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9NWZ3
Elsewhere: RCSB PDB 4YP8 · PDBe 4YP8 · UniProt Q9NWZ3

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