MolNFT v1 · #134674 · protein

Structure-based optimization of 1H-imidazole-2-carboxamides as axl kinase inhibitors utilizing a mer mutant surrogate

5TC0 · Tyrosine-protein kinase mer: “Structure-based optimization of 1H-imidazole-2-carboxamides as axl kinase inhibitors utilizing a mer mutant…”. X-ray diffraction, 1 ligand (79Y), 5 pockets (best druggability 0.66). MolNFT v1 #134674 on…

PDB: 5TC0
Type: protein
Length: 488 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: 79Y
Pockets: 5 · best druggability 0.66

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	238	37% helix, 21% strand	Q12866
B	Tyrosine-protein kinase mer (EC 2.7.10.1)	protein	250	43% helix, 16% strand	Q12866

Ligands and binding sites

79Y · N-(2-{4-[(2S)-4-(methylsulfonyl)morpholin-2-yl]-1,3-thiazol-2-yl}phenyl)-1H-imidazole-2-carboxamide · ligand · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	325	0.66	0.81	35	empty
2	390	0.64	0.78	35	79Y
3	226	0.49	0.75	37	empty
4	150	0.47	0.77	18	empty
5	110	0.46	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 965 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5TC0 · Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors… · 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 A 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 Q12866
Elsewhere: RCSB PDB 5TC0 · PDBe 5TC0 · UniProt Q12866

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