5UPZ: Protease

HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group. Determined by X-ray diffraction at 1.27 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 1.27 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,968
Mol. weight: 22.48 kDa
Ligands: 8HD
Released: 10 May 2017

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

Secondary structure: helices and β-sheets

5UPZ contains 2 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: 1 helix, 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	43-49	7	2
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
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
Protease	A, B	protein	99	Human immunodeficiency virus 1	P03366

Sequence of entity 1 (A, B), FASTA

>5UPZ_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
8HD	N~3~-{(2S,3R)-3-hydroxy-4-[{[4-(hydroxymethyl)phenyl]sulfonyl}(2-methylpropyl)a…	C35 H42 N4 O7 S	1

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

Primary citation

Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex. Ghosh, A.K., Brindisi, M., Nyalapatla, P.R. et al. Bioorg Med Chem (2017) 25:5114-5127. DOI 10.1016/j.bmc.2017.04.005 · PubMed

Other PDB entries of the same protein (UniProt P03366), best resolution first:

2HS1 0.84 Å, Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114…
3NU3 1.02 Å, Wild Type HIV-1 Protease with Antiviral Drug Amprenavir
2IDW 1.1 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide…
4ZIP 1.11 Å, HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)
3NU6 1.16 Å, Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir
5JG1 1.16 Å, HIV-1 wild Type protease with GRL-031-14A (a Adamantane P1-Ligand with…
3NU4 1.2 Å, Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Drug Amprenavir
5AGZ 1.2 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
6PRF 1.21 Å, HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A
2HS2 1.22 Å, Crystal structure of M46L mutant of HIV-1 protease complexed with TMC114 (darunavir)
5AH8 1.26 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
3OK9 1.27 Å, Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor…

Browse structure collections

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