MolNFT v1 · #101668 · protein

HIV integrase in complex with inhibitor

4NYF: “HIV integrase in complex with inhibitor”. X-ray diffraction, 2 ligands (4BI, CD), 5 pockets (best druggability 0.49). MolNFT v1 #101668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NYF
Type: protein
Length: 289 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
EC: 2.7.7.-
UniProt: P0C6F2
Ligands: 4BI, CD
Pockets: 5 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase (EC 2.7.7.-)	protein	149	50% helix, 19% strand	P0C6F2
B	Integrase (EC 2.7.7.-)	protein	140	48% helix, 23% strand	P0C6F2

Ligands and binding sites

4BI · (2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid · ligand · chains A, B
CD · Cadmium ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.49	0.79	25	empty
2	151	0.48	0.77	24	empty
3	99	0.43	0.78	16	empty
4	82	0.39	0.78	23	empty
5	103	0.38	0.75	16	4BI

Interfaces

1 interface between chains.

A–B · 1567 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4NYF · HIV integrase in complex with inhibitor · 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 P0C6F2
Elsewhere: RCSB PDB 4NYF · PDBe 4NYF · UniProt P0C6F2

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