Structure of PDB 1ivp Chain B Binding Site BS01

Receptor Information
>1ivp Chain B (length=99) Species: 11709 (Human immunodeficiency virus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTLEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL
Ligand information
Ligand ID1ZK
InChIInChI=1S/C45H61N7O7/c1-5-29(4)40(45(58)48-25-32-18-11-12-21-47-32)52-44(57)39(28(2)3)42(55)41(54)35(22-30-14-7-6-8-15-30)51-43(56)36(23-33-24-46-27-49-33)50-38(53)26-59-37-20-13-17-31-16-9-10-19-34(31)37/h9-13,16-21,24,27-30,35-36,39-42,54-55H,5-8,14-15,22-23,25-26H2,1-4H3,(H,46,49)(H,48,58)(H,50,53)(H,51,56)(H,52,57)/p+1/t29-,35-,36-,39+,40-,41+,42+/m0/s1
InChIKeyZTKCGLWIXHAITR-JIFWBGJESA-O
SMILES
SoftwareSMILES
CACTVS 3.341CC[C@H](C)[C@H](NC(=O)[C@H](C(C)C)[C@@H](O)[C@H](O)[C@H](CC1CCCCC1)NC(=O)[C@H](Cc2c[nH]c[nH+]2)NC(=O)COc3cccc4ccccc34)C(=O)NCc5ccccn5
CACTVS 3.341CC[CH](C)[CH](NC(=O)[CH](C(C)C)[CH](O)[CH](O)[CH](CC1CCCCC1)NC(=O)[CH](Cc2c[nH]c[nH+]2)NC(=O)COc3cccc4ccccc34)C(=O)NCc5ccccn5
ACDLabs 10.04O=C(NCc1ncccc1)C(NC(=O)C(C(C)C)C(O)C(O)C(NC(=O)C(NC(=O)COc3c2ccccc2ccc3)Cc4cnc[nH+]4)CC5CCCCC5)C(C)CC
OpenEye OEToolkits 1.5.0CCC(C)C(C(=O)NCc1ccccn1)NC(=O)C(C(C)C)C(C(C(CC2CCCCC2)NC(=O)C(Cc3c[nH]c[nH+]3)NC(=O)COc4cccc5c4cccc5)O)O
OpenEye OEToolkits 1.5.0CC[C@H](C)[C@@H](C(=O)NCc1ccccn1)NC(=O)[C@H](C(C)C)[C@H]([C@@H]([C@H](CC2CCCCC2)NC(=O)[C@H](Cc3c[nH]c[nH+]3)NC(=O)COc4cccc5c4cccc5)O)O
FormulaC45 H62 N7 O7
Name4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium;
U75875
ChEMBL
DrugBank
ZINC
PDB chain1ivp Chain B Residue 100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ivp The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
D25 A28 D29 D30 V47 G48 G49
Binding residue
(residue number reindexed from 1)
D25 A28 D29 D30 V47 G48 G49
Annotation score1
Binding affinityMOAD: Ki=30nM
PDBbind-CN: -logKd/Ki=7.52,Ki=30nM
Enzymatic activity
Catalytic site (original residue number in PDB) D25 T26 G27
Catalytic site (residue number reindexed from 1) D25 T26 G27
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.47: HIV-2 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function

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Biological Process
External links
PDB RCSB:1ivp, PDBe:1ivp, PDBj:1ivp
PDBsum1ivp
PubMed8514751
UniProtP04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)

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