MolNFT v1 · #144423 · protein

Crystal structure of rheb in complex with compound NR1

6BT0 · GTP-binding protein rheb: “Crystal structure of rheb in complex with compound NR1”. X-ray diffraction, 3 ligands (GDP, E7V, MG), 9 pockets (best druggability 0.79). MolNFT v1 #144423 on GenesisL1: 3D structure, binding sites and…

PDB: 6BT0
Type: protein
Length: 673 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein rheb
UniProt: Q15382
Ligands: GDP, E7V, MG
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding protein rheb	protein	169	34% helix, 26% strand	Q15382
B, C, D	GTP-binding protein rheb	protein	168	33% helix, 26% strand	Q15382

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
E7V · 4-bromo-6-[(3,4-dichlorophenyl)sulfanyl]-1-{[4-(dimethylcarbamoyl)phenyl]methyl}-1H-indole-2-carboxylic acid · ligand · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	926	0.79	0.81	99	MG, GDP
2	902	0.75	0.79	70	MG, GDP
3	205	0.54	0.78	25	empty
4	71	0.48	0.83	14	empty
5	126	0.45	0.77	19	empty

Interfaces

4 interfaces between chains.

B–C · 453 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 438 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 366 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 70 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6BT0 · Crystal structure of rheb in complex with compound NR1 · the same entry in another collection · chain A against A, TM-score 1.00
Q15382 · AlphaFold monomer V2.0 prediction for GTP-binding protein rheb (Q15382) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q15382
Elsewhere: RCSB PDB 6BT0 · PDBe 6BT0 · UniProt Q15382

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