MolNFT v1 · #167440 · protein

Co-crystal structure of gs-6207 bound to HIV-1 capsid hexamer

6VKV · Capsid protein P24: “Co-crystal structure of gs-6207 bound to HIV-1 capsid hexamer”. X-ray diffraction, 3 ligands (QNG, CL, IOD), 5 pockets (best druggability 0.38). MolNFT v1 #167440 on GenesisL1: 3D structure, binding sites and…

PDB: 6VKV
Type: protein
Length: 660 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24
UniProt: B6DRA0
Ligands: QNG, CL, IOD
Pockets: 5 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Capsid protein P24	protein	220	58% helix, 3% strand	B6DRA0

Ligands and binding sites

QNG · N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2, 2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bs,4ar)-5,5-difluoro-3-(trifluoromethyl)-3B,4,4A,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide · ligand · 3 copies · chains A, B, C
CL · Chloride ion · ion · 14 copies · chains A, B, C
IOD · Iodide ion · ion · 5 copies · chains A, B, C

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	89	0.38	0.77	17	QNG
2	76	0.33	0.75	16	empty
3	66	0.32	0.76	16	empty
4	64	0.29	0.74	15	empty
5	55	0.27	0.73	16	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6VKV · Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer · 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 B6DRA0
Elsewhere: RCSB PDB 6VKV · PDBe 6VKV · UniProt B6DRA0

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