5DGU: Pol protein

Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted fused-Tetrahydropyranyl Tetrahydrofuran as P2-Ligand GRL-004-11A. Determined by X-ray diffraction at 1.22 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 1.22 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,920
Mol. weight: 22.3 kDa
Ligands: 5B7
Released: 28 Oct 2015

Explore 5DGU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DGU contains 3 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	31-33	3	2
β-strand	42-49	8	2
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
α-helix	91-93	3
β-strand	96-98	3	1

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	3
β-strand	18-24	7	3
β-strand	32-33	2	3
β-strand	43-49	7	3
β-strand	52-66	15	3
β-strand	69-77	9	3
β-strand	84-85	2	3
α-helix	87-90	4
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pol protein	A, B	protein	99	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DGU_1 Pol protein (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
5B7	(3R,3aR,4S,7aS)-3-methoxyhexahydro-4H-furo[2,3-b]pyran-4-yl…	C30 H42 N2 O9 S	1

Water and common crystallization additives (NA, ACT, CL) are not listed.

Primary citation

Design, synthesis, biological evaluation and X-ray structural studies of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran as P2-ligands. Ghosh, A.K., Martyr, C.D., Kassekert, L.A. et al. Org Biomol Chem (2015) 13:11607-11621. DOI 10.1039/c5ob01930c · PubMed

Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DV4 1.14 Å, HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with…
6DIF 1.2 Å, Wild-type HIV-1 protease in complex with tipranavir
6DV0 1.2 Å, HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine…
6E9A 1.22 Å, HIV-1 wild type protease with grl-034-17A, (3aS, 5R, 6aR)-2-oxohexahyd…
6DJ1 1.26 Å, Wild-type HIV-1 protease in complex with Lopinavir
8F0F 1.29 Å, HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on…
6E7J 1.3 Å, HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one…
6DJ7 1.31 Å, HIV-1 protease with mutation L76V in complex with GRL-5010…
8ESX 1.35 Å, HIV protease in complex with benzoxaborolone analog of darunavir
8ESY 1.35 Å, D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…

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