Structure of PDB 6kdo Chain C Binding Site BS02

Receptor Information
>6kdo Chain C (length=552) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
QKKSVTVLDVGDAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPM
GWKGSPAIMQSSMTKILEPFRKQNPDIVIYQYVDDLYVGSDLEIGQHRTK
IEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDS
WTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAEL
ELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKT
GKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAW
WTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRETK
LGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQY
ALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKL
VS
Ligand information
Ligand ID1RZ
InChIInChI=1S/C8H14N3O12P3S/c9-5-1-2-11(8(12)10-5)6-4-27-7(21-6)3-20-25(16,17)23-26(18,19)22-24(13,14)15/h1-2,6-7H,3-4H2,(H,16,17)(H,18,19)(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1
InChIKeyYLEQMGZZMCJKCN-NKWVEPMBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC8 H14 N3 O12 P3 S
NameLamivudine Triphosphate;
Lamivudine-5'-triphosphate;
3TC Triphosphate;
[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBLCHEMBL1230
DrugBank
ZINC
PDB chain6kdo Chain C Residue 601 [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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PDB6kdo Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Resolution2.573 Å
Binding residue
(original residue number in PDB)
R72 F115 D185
Binding residue
(residue number reindexed from 1)
R71 F114 D184
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:0003676 nucleic acid binding
GO:0003964 RNA-directed DNA polymerase activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
Biological Process
GO:0006278 RNA-templated DNA biosynthetic process

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Molecular Function

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Biological Process
External links
PDB RCSB:6kdo, PDBe:6kdo, PDBj:6kdo
PDBsum6kdo
PubMed32080249
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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