MolNFT v1 · #87917 · protein

Interrogating HIV integrase for compounds that bind- a sampl challenge

4CFC: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 3 ligands (7NV, SO4, CL), 7 pockets (best druggability 0.65). MolNFT v1 #87917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CFC
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: 7NV, SO4, CL
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Integrase (EC 2.7.7.7)	protein	149	53% helix, 19% strand	Q76353

Ligands and binding sites

7NV · 5-[[[(1S)-2-(butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
CL · Chloride ion · ion · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.65	0.83	29	SO4, ACT
2	106	0.52	0.82	23	CL
3	103	0.49	0.81	21	CL
4	172	0.47	0.76	29	empty
5	100	0.42	0.77	16	7NV

Interfaces

1 interface between chains.

A–B · 1480 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4CFC · 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 4CFC · PDBe 4CFC · UniProt Q76353

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