Structure of PDB 6oyd Chain A Binding Site BS01

Receptor Information
>6oyd Chain A (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]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDNKA
InChIInChI=1S/C33H43FN4O8S/c1-18(2)14-38(47(41,42)23-9-10-26-29(13-23)45-32(36-26)35-19(3)4)15-28(39)27(11-20-5-7-22(34)8-6-20)37-33(40)46-30-21-12-24-25(30)17-44-31(24)43-16-21/h5-10,13,18-19,21,24-25,27-28,30-31,39H,11-12,14-17H2,1-4H3,(H,35,36)(H,37,40)/t21-,24-,25-,27+,28-,30+,31+/m1/s1
InChIKeyWQIWHYJHYCEVFO-BLFKHSGCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)CN(C[C@@H](O)[C@H](Cc1ccc(F)cc1)NC(=O)O[C@H]2[C@H]3CO[C@H]4OC[C@@H]2[C@H]4C3)[S](=O)(=O)c5ccc6nc(NC(C)C)oc6c5
ACDLabs 12.01C12CC3COC1OCC2C3OC(=O)NC(Cc4ccc(cc4)F)C(O)CN(CC(C)C)S(=O)(=O)c5cc6c(cc5)nc(o6)NC(C)C
CACTVS 3.385CC(C)CN(C[CH](O)[CH](Cc1ccc(F)cc1)NC(=O)O[CH]2[CH]3CO[CH]4OC[CH]2[CH]4C3)[S](=O)(=O)c5ccc6nc(NC(C)C)oc6c5
OpenEye OEToolkits 2.0.7CC(C)CN(C[C@H]([C@H](Cc1ccc(cc1)F)NC(=O)O[C@H]2[C@@H]3C[C@@H]4[C@H]2CO[C@@H]4OC3)O)S(=O)(=O)c5ccc6c(c5)oc(n6)NC(C)C
OpenEye OEToolkits 2.0.7CC(C)CN(CC(C(Cc1ccc(cc1)F)NC(=O)OC2C3CC4C2COC4OC3)O)S(=O)(=O)c5ccc6c(c5)oc(n6)NC(C)C
FormulaC33 H43 F N4 O8 S
Name(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl {(2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-[(2-methylpropyl)({2-[(propan-2-yl)amino]-1,3-benzoxazol-6-yl}sulfonyl)amino]butan-2-yl}carbamate
ChEMBL
DrugBank
ZINC
PDB chain6oyd Chain A Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6oyd Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 P81 V82
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 P81 V82
Annotation score1
Binding affinityMOAD: ic50=0.12nM
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.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6oyd, PDBe:6oyd, PDBj:6oyd
PDBsum6oyd
PubMed32606378
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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