MolNFT v1 · #87905 · protein

Interrogating HIV integrase for compounds that bind- a sampl challenge

4CF0: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 2 ligands (O5U, SO4), 7 pockets (best druggability 0.66). MolNFT v1 #87905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CF0
Type: protein
Length: 298 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: O5U, SO4
Pockets: 7 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Integrase (EC 2.7.7.7)	protein	149	53% helix, 21% strand	Q76353

Ligands and binding sites

O5U · (2R)-6-[[(1R,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
ACT · Acetate ion · additive · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.66	0.84	31	SO4, ACT
2	102	0.52	0.83	22	empty
3	110	0.51	0.81	21	empty
4	176	0.47	0.76	28	empty
5	110	0.45	0.78	17	O5U

Interfaces

1 interface between chains.

A–B · 1494 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4CF0 · 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 4CF0 · PDBe 4CF0 · UniProt Q76353

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