MolNFT v2 · #226295 · protein

HIV-1 integrase core domain in complex with compound 15

8ZHA: “HIV-1 integrase core domain in complex with compound 15”. X-ray diffraction at 1.95, 2 ligands (A1L1W, SO4), 1 pocket (best druggability 0.26). MolNFT v2 #226295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8ZHA
Type: protein
Length: 143 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.95
Source: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Molecule: Integrase
EC: 2.7.7.-, 3.1.-.-
UniProt: P12497
Ligands: A1L1W, SO4
Pockets: 1 · best druggability 0.26

Structure

x-ray diffraction · resolution 1.95 · 1 distinct chain · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase (EC 2.7.7.-, 3.1.-.-)	protein	143	49% helix, 20% strand	P12497

Ligands and binding sites

A1L1W · (2~{S})-2-[7-(cycloheptylcarbamoyl)-4',5-dimethyl-spiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.26	0.72	10	empty

Modifications

Observed in the structure: 3 modified (nonstandard).

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 P12497
Elsewhere: RCSB PDB 8ZHA · PDBe 8ZHA · UniProt P12497

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