MolNFT v1 · #124165 · protein

IRAK4 in complex with compound 1

5K75 · Interleukin-1 receptor-associated kinase 4: “IRAK4 in complex with compound 1”. X-ray diffraction, 2 ligands (6QX, SO4), 16 pockets (best druggability 0.82). MolNFT v1 #124165 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5K75
Type: protein
Length: 1,115 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: 6QX, SO4
Pockets: 16 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	273	41% helix, 16% strand	Q9NWZ3
B	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	276	41% helix, 16% strand	Q9NWZ3
C	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	284	43% helix, 17% strand	Q9NWZ3
D	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1)	protein	282	43% helix, 17% strand	Q9NWZ3

Ligands and binding sites

6QX · ~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 7 copies · chains B, D, A, C

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.82	0.90	66	empty
2	325	0.81	0.91	42	empty
3	810	0.73	0.78	51	empty
4	223	0.71	0.87	35	6QX
5	231	0.71	0.87	36	6QX

Interfaces

5 interfaces between chains.

A–D · 676 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 618 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 564 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 562 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 438 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (phosphorylation).

Compared structures

5K75 · IRAK4 in complex with Compound 1 · 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 5K75 · PDBe 5K75 · UniProt Q9NWZ3

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