MolNFT v1 · #165410 · protein

The pH domain of BRUTON'S tyrosine kinase mutant R28C

6TUH · Tyrosine-protein kinase btk: “The pH domain of BRUTON'S tyrosine kinase mutant R28C”. X-ray diffraction, 3 ligands (NXT, ZN, MG), 11 pockets (best druggability 0.62). MolNFT v1 #165410 on GenesisL1: 3D structure, binding sites and…

PDB: 6TUH
Type: protein
Length: 607 residues
Chains: 4
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: NXT, ZN, MG
Pockets: 11 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase btk (EC 2.7.10.2)	protein	157	15% helix, 37% strand	Q06187
B	Tyrosine-protein kinase btk (EC 2.7.10.2)	protein	156	15% helix, 38% strand	Q06187
C, D	Tyrosine-protein kinase btk (EC 2.7.10.2)	protein	147	16% helix, 37% strand	Q06187

Ligands and binding sites

NXT · 4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid · ligand · 5 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · chains A, B

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

Pockets

11 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	146	0.62	0.85	30	empty
2	386	0.60	0.76	27	empty
3	92	0.51	0.83	21	empty
4	77	0.48	0.83	19	empty
5	190	0.47	0.75	26	empty

Interfaces

4 interfaces between chains.

A–B · 1092 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 485 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 237 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 49 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

6TUH · PH domain of Bruton's tyrosine kinase bound to compound 1 · the same entry in another collection · chain D against D, TM-score 1.00
Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain D 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 Q06187
Elsewhere: RCSB PDB 6TUH · PDBe 6TUH · UniProt Q06187

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