MolNFT v1 · #124176 · protein

IRAK4 in complex with AZ3862

5K7G · Interleukin-1 receptor-associated kinase 4: “IRAK4 in complex with AZ3862”. X-ray diffraction, 2 ligands (6R0, SO4), 11 pockets (best druggability 0.85). MolNFT v1 #124176 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5K7G
Type: protein
Length: 1,124 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: 6R0, SO4
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 3 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	279	40% helix, 18% strand	Q9NWZ3
B	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	275	42% helix, 16% strand	Q9NWZ3
C, D	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	285	41% helix, 17% strand	Q9NWZ3

Ligands and binding sites

6R0 · (3~{a}~{S},7~{a}~{R})-1-methyl-5-[4-[[5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]amino]cyclohexyl]-3,3~{a},4,6,7,7~{a}-hexahydropyrrolo[3,2-c]pyridin-2-one · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains A, B, D

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.85	0.86	136	6R0
2	685	0.81	0.86	83	empty
3	781	0.73	0.79	51	empty
4	799	0.73	0.78	49	empty
5	295	0.70	0.84	37	6R0

Interfaces

5 interfaces between chains.

B–C · 621 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 619 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 584 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 530 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 255 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (phosphorylation).

Compared structures

5K7G · IRAK4 in complex with AZ3862 · 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 5K7G · PDBe 5K7G · UniProt Q9NWZ3

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