MolNFT v1 · #173317 · protein

Mertk kinase domain in complex with nps-1034

7AVX · Tyrosine-protein kinase mer: “Mertk kinase domain in complex with nps-1034”. X-ray diffraction, 1 ligand (S4K), 3 pockets (best druggability 0.75). MolNFT v1 #173317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7AVX
Type: protein
Length: 539 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein kinase mer
EC: 2.7.10.1
UniProt: Q12866
Ligands: S4K
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase mer (EC 2.7.10.1)	protein	276	39% helix, 17% strand	Q12866
B	Tyrosine-protein kinase mer (EC 2.7.10.1)	protein	263	41% helix, 19% strand	Q12866

Ligands and binding sites

S4K · 1-(4-fluorophenyl)-N-[3-fluoro-4-[(3-phenyl-1H-pyrrolo[2,3-b]pyridin-4-yl)oxy]phenyl]-2,3-dimethyl-5-oxopyrazole-4-carboxamide · ligand · 2 copies · chains A, B

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

Pockets

3 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	880	0.75	0.79	94	S4K
2	575	0.69	0.78	54	S4K
3	219	0.59	0.80	21	empty

Interfaces

1 interface between chains.

A–B · 1048 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7AVX · MerTK kinase domain in complex with NPS-1034 · the same entry in another collection · chain A against A, TM-score 1.00
Q12866 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase mer (Q12866) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 Q12866
Elsewhere: RCSB PDB 7AVX · PDBe 7AVX · UniProt Q12866

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