Structure of PDB 6kdj Chain A Binding Site BS02

Receptor Information
>6kdj Chain A (length=553) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KQKKSVTVLDVGDAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLP
MGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEA
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRET
KLGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVS
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 chain6kdj Chain A 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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PDB6kdj Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Resolution2.51 Å
Binding residue
(original residue number in PDB)
R72 V111 G112 D113 A114 M151 M184 D185
Binding residue
(residue number reindexed from 1)
R72 V111 G112 D113 A114 M151 M184 D185
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

View graph for
Biological Process
External links
PDB RCSB:6kdj, PDBe:6kdj, PDBj:6kdj
PDBsum6kdj
PubMed32080249
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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