MolNFT v1 · #169188 · protein

Co-structure of btk kinase domain with L-005191930 inhibitor

6X3O · Tyrosine-protein kinase btk: “Co-structure of btk kinase domain with L-005191930 inhibitor”. X-ray diffraction, 2 ligands (ULY, 5WE), 4 pockets (best druggability 0.80). MolNFT v1 #169188 on GenesisL1: 3D structure, binding sites…

PDB: 6X3O
Type: protein
Length: 532 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein kinase btk
EC: 2.7.10.2
UniProt: Q06187
Ligands: ULY, 5WE
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase btk (EC 2.7.10.2)	protein	265	43% helix, 17% strand	Q06187
B	Tyrosine-protein kinase btk (EC 2.7.10.2)	protein	267	43% helix, 17% strand	Q06187

Ligands and binding sites

ULY · 4-{8-amino-3-[(6R,8aS)-3-oxo-3,5,6,7,8,8a-hexahydroindolizin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-3-methoxy-N-[4-(trifluoromethyl)pyridin-2-yl]benzamide · ligand · 2 copies · chains A, B
5WE · 4-[8-azanyl-3-[(2~{S})-1-[4-(dimethylamino) butanoyl]pyrrolidin-2-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-(1,3-thiazol-2-yl)benzamide · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.80	0.86	71	ULY
2	429	0.78	0.86	63	ULY
3	195	0.56	0.79	27	empty
4	69	0.32	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 473 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6X3O · Co-structure of BTK kinase domain with L-005191930 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q06187
Elsewhere: RCSB PDB 6X3O · PDBe 6X3O · UniProt Q06187

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