MolNFT v1 · #88068 · protein

Interrogating HIV integrase for compounds that bind- a sampl challenge

4CJQ: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 2 ligands (VXO, SO4), 7 pockets (best druggability 0.64). MolNFT v1 #88068 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CJQ
Type: protein
Length: 296 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
EC: 2.7.7.7
UniProt: Q76353
Ligands: VXO, SO4
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Integrase (EC 2.7.7.7)	protein	148	53% helix, 20% strand	Q76353

Ligands and binding sites

VXO · 5-[(2S)-2-[[2-(1H-indol-3-yl)ethanoylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.64	0.82	28	ACT, SO4
2	110	0.51	0.82	25	empty
3	95	0.49	0.82	18	empty
4	106	0.43	0.77	17	VXO
5	147	0.42	0.75	30	empty

Interfaces

1 interface between chains.

A–B · 1484 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4CJQ · Interrogating HIV integrase for compounds that bind- a SAMPL challenge · 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 Q76353
Elsewhere: RCSB PDB 4CJQ · PDBe 4CJQ · UniProt Q76353

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.