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Crystal structure of human KRAS G12C covalently bound with araxes WO2020/028706A1 compound I-1

Analyse Crystal structure of human KRAS G12C covalently bound with araxes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8DNI
Type: protein
Length: 170 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, U4L, MG
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase KRAS	protein	170	38% helix, 25% strand	P01116

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
U4L · (4P)-4-(5-methyl-1H-indazol-4-yl)-6-(2-propanoyl-2,6-diazaspiro[3.4]octan-6-yl)-2-(pyrrolidin-1-yl) pyrimidine-5-carbonitrile · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	410	0.67	0.80	46	MG, GDP, U4L

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

8DNI · Crystal structure of human KRAS G12C covalently bound with Araxes WO2020/028706A1… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt P01116
Elsewhere: RCSB PDB 8DNI · PDBe 8DNI · UniProt P01116

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