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Crystal structure of small molecule disulfide 2C07 bound to K-RAS cys light M72C GDP

Analyse Crystal structure of small molecule disulfide 2C07 bound to K-RAS cys light… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VBM
Type: protein
Length: 168 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, 92V, MG
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase KRAS	protein	168	38% helix, 26% strand	P01116

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
92V · 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide · 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

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.48	0.79	27	MG, GDP
2	56	0.38	0.80	14	empty

Modifications

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

Compared structures

5VBM · Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C GDP · the same entry in another collection · chain A against A, TM-score 1.00

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 P01116
Elsewhere: RCSB PDB 5VBM · PDBe 5VBM · UniProt P01116

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