Structure of PDB 6uir Chain A Binding Site BS03

Receptor Information

>6uir Chain A (length=544) Species: 11706 (HIV-1 M:B_HXB2R)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKK
SVTVLDVGDAYFSVPLDEDFRKYTAFTIPIRYQYNVLPQGWKGSPAIFQS
SMTKILEPFRKQNPDIVIYQYVDDLYVGSDLEIGQHRTKIEELRQHLLRW
GLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDICKLVG
KLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKE
PVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHT
NDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIP
EWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRG
RQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQ
SESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI

Ligand information

• Ligand ID: 1RY
• InChI: InChI=1S/C8H13FN3O12P3S/c9-4-1-12(8(13)11-7(4)10)5-3-28-6(22-5)2-21-26(17,18)24-27(19,20)23-25(14,15)16/h1,5-6H,2-3H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m0/s1
• InChIKey: WIEOLFZNMKSGEX-NTSWFWBYSA-N
• SMILES:
  CACTVS 3.370: NC1=NC(=O)N(C=C1F)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
  OpenEye OEToolkits 1.7.6: C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
  CACTVS 3.370: NC1=NC(=O)N(C=C1F)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
  OpenEye OEToolkits 1.7.6: C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
• Formula: C8 H13 F N3 O12 P3 S
• Name: [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
• ChEMBL: CHEMBL341421
• PDB chain: 6uir Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6uir Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance.
• Resolution: 2.639 Å
• Binding residue (original residue number in PDB): K65 R72 G112 D113 Y115 Q151 V184 K220
• Binding residue (residue number reindexed from 1): K65 R68 G108 D109 Y111 Q139 V172 K208
• Annotation score: 1

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

External links

• PDB: RCSB:6uir, PDBe:6uir, PDBj:6uir
• PDBsum: 6uir
• PubMed: 31872074
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)