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Approach for targeting RAS with small molecules that activate sos- mediated nucleotide exchange

Analyse Approach for targeting RAS with small molecules that activate sos- mediated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NYI
Type: protein
Length: 806 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase HRAS; Son of sevenless homolog 1
UniProt: P01112, Q07889
Ligands: GNP, 2PX, MG
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	GTPase HRAS	protein	167	37% helix, 26% strand	P01112
R	GTPase HRAS	protein	167	37% helix, 26% strand	P01112
S	Son of sevenless homolog 1	protein	472	57% helix, 4% strand	Q07889

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
2PX · N-{1-[(5-methyl-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide · ligand · chains S
MG · Magnesium ion · metal · chains Q

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	817	0.81	0.84	91	MG, GNP
2	241	0.72	0.87	41	empty
3	50	0.66	0.96	16	empty
4	229	0.56	0.78	42	empty
5	217	0.52	0.76	30	empty

Interfaces

2 interfaces between chains.

R–S · 1857 Å² buried · 23 hydrogen bonds · protein-protein
Q–S · 1724 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

4NYI · Approach for Targeting Ras with Small Molecules that Activate SOS-Mediated Nucleotide… · the same entry in another collection · chain Q against Q, TM-score 1.00
Q07889 · AlphaFold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) · a predicted model of the same protein · chain S against A, TM-score 0.93

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 P01112
Every structure of UniProt Q07889
Elsewhere: RCSB PDB 4NYI · PDBe 4NYI · UniProt P01112 · UniProt Q07889

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