MolNFT v1 · #146036 · protein

RAS:SOS:RAS in complex with a small molecule activator

6D5M · GTPase HRAS: “RAS:SOS:RAS in complex with a small molecule activator”. X-ray diffraction, 3 ligands (GNP, FW4, MG), 13 pockets (best druggability 0.78). MolNFT v1 #146036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D5M
Type: protein
Length: 801 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, FW4, MG
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	GTPase HRAS	protein	166	39% helix, 27% strand	P01112
R	GTPase HRAS	protein	167	34% helix, 25% strand	P01112
S	Son of sevenless homolog 1	protein	468	56% helix, 4% strand	Q07889

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
FW4 · 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-2-(piperazin-1-yl)-1H-benzimidazole · 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

13 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	1027	0.78	0.80	102	MG, GNP
2	283	0.70	0.85	46	empty
3	55	0.66	0.95	17	empty
4	109	0.60	0.86	28	empty
5	136	0.57	0.83	19	FW4

Interfaces

2 interfaces between chains.

R–S · 1782 Å² buried · 25 hydrogen bonds · protein-protein
Q–S · 1513 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6D5M · Ras:SOS:Ras in complex with a small molecule activator · 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 6D5M · PDBe 6D5M · UniProt P01112 · UniProt Q07889

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