Structure of PDB 6c8x Chain B Binding Site BS01

Receptor Information
>6c8x Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDBVR
InChIInChI=1S/C27H36BN2O9S/c1-18(2)15-30(40(35,36)21-10-8-20(9-11-21)28(33)34)16-24(31)23(14-19-6-4-3-5-7-19)29-27(32)39-25-17-38-26-22(25)12-13-37-26/h3-11,18,22-26,31,33H,12-17H2,1-2H3,(H,29,32)/t22-,23-,24+,25-,26+/m0/s1
InChIKeyQKKZROKMILDVQY-HEXNFIEUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6B(=O)(c1ccc(cc1)S(=O)(=O)N(C[C@H]([C@H](Cc2ccccc2)NC(=O)O[C@H]3CO[C@@H]4[C@H]3CCO4)O)CC(C)C)O
CACTVS 3.385CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc(cc4)[B](O)=O
OpenEye OEToolkits 2.0.6B(=O)(c1ccc(cc1)S(=O)(=O)N(CC(C)C)CC(C(Cc2ccccc2)NC(=O)OC3COC4C3CCO4)O)O
CACTVS 3.385CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc(cc4)[B](O)=O
FormulaC27 H36 B N2 O9 S
Name
ChEMBL
DrugBank
ZINC
PDB chain6c8x Chain A Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6c8x Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid.
Resolution1.613 Å
Binding residue
(original residue number in PDB)		D125 G127 D129 G148 G149 I150
Binding residue
(residue number reindexed from 1)		D25 G27 D29 G48 G49 I50
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=12.30,Ki=0.5pM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
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.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6c8x, PDBe:6c8x, PDBj:6c8x
PDBsum6c8x
PubMed30346745
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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