MolNFT v1 · #99881 · protein

Selective activation of EPAC1 and EPAC2

4MGZ · Rap guanine nucleotide exchange factor 4: “Selective activation of EPAC1 and EPAC2”. X-ray diffraction, 2 ligands (HR6, SO4), 10 pockets (best druggability 0.77). MolNFT v1 #99881 on GenesisL1: 3D structure, binding sites and…

PDB: 4MGZ
Type: protein
Length: 782 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rap guanine nucleotide exchange factor 4; RAS-related protein rap-1B
UniProt: Q9EQZ6, P61224
Ligands: HR6, SO4
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Rap guanine nucleotide exchange factor 4	protein	632	53% helix, 15% strand	Q9EQZ6
R	RAS-related protein rap-1B	protein	150	35% helix, 21% strand	P61224

Ligands and binding sites

HR6 · (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide · ligand · 2 copies · chains E
SO4 · Sulfate ion · ion · chains R

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	1061	0.77	0.79	81	SO4
2	314	0.75	0.87	38	HR6
3	148	0.53	0.80	29	empty
4	99	0.52	0.83	25	empty
5	164	0.51	0.78	22	empty

Interfaces

1 interface between chains.

E–R · 1588 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4MGZ · Selective activation of Epac1 and Epac2 · the same entry in another collection · chain E against E, TM-score 1.00
P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain R against A, TM-score 0.88
Q9EQZ6 · AlphaFold monomer V2.0 prediction for rap guanine nucleotide exchange factor 4 (Q9EQZ6) · a predicted model of the same protein · chain E against A, TM-score 0.78

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 Q9EQZ6
Every structure of UniProt P61224
Elsewhere: RCSB PDB 4MGZ · PDBe 4MGZ · UniProt Q9EQZ6 · UniProt P61224

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