Structure of PDB 6kdk Chain B Binding Site BS02

Receptor Information
>6kdk Chain B (length=406) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPEN
PYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKQKK
SVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK
GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEE
LRQHLLRWGGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIY
AGIKVRQLSKLLRGTKALTEVVPLTEEAELELAENREILKEPVHGVYYDP
SKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMKGAHTNDVKQLTEA
VQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPP
LVKLWY
Ligand information
Ligand IDGLC
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
InChIKeyWQZGKKKJIJFFOK-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-glucopyranose;
alpha-D-glucose;
D-glucose;
glucose
ChEMBLCHEMBL423707
DrugBank
ZINCZINC000003861213
PDB chain6kdk Chain G Residue 1 [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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PDB6kdk Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Resolution2.56 Å
Binding residue
(original residue number in PDB)		R78 E79 K82 E413 W414
Binding residue
(residue number reindexed from 1)		R74 E75 K78 E392 W393
Annotation score1
Enzymatic activity
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:0003964 RNA-directed DNA polymerase activity
Biological Process
GO:0006278 RNA-templated DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6kdk, PDBe:6kdk, PDBj:6kdk
PDBsum6kdk
PubMed32080249
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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