Structure of PDB 6ika Chain C Binding Site BS02

Receptor Information

>6ika Chain C (length=553) Species: 11676 (Human immunodeficiency virus 1)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KQKKSVTVLDVSAAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLP
MGWKGSPALLQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEA
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRET
KLGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVS

Ligand information

• Ligand ID: ET9
• InChI: InChI=1S/C12H18N5O12P3/c1-5-6(3-27-31(23,24)29-32(25,26)28-30(20,21)22)8(18)2-7(5)17-4-14-9-10(17)15-12(13)16-11(9)19/h4,6-8,18H,1-3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,13,15,16,19)/t6-,7-,8-/m0/s1
• InChIKey: YMBBDUCQYPKKJK-FXQIFTODSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: C=C1C(CC(C1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)n2cnc3c2NC(=NC3=O)N
  OpenEye OEToolkits 2.0.6: C=C1[C@H](C[C@@H]([C@H]1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)n2cnc3c2NC(=NC3=O)N
  CACTVS 3.385: NC1=NC(=O)c2ncn([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1
  CACTVS 3.385: NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1
• Formula: C12 H18 N5 O12 P3
• Name: [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate;
  Entecavir 5'-triphosphate
• PDB chain: 6ika Chain C Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ika Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors.
• Resolution: 2.598 Å
• Binding residue (original residue number in PDB): R72 S112 A113 F115 M184 D185
• Binding residue (residue number reindexed from 1): R72 S112 A113 F115 M184 D185
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.26.13: retroviral ribonuclease H.

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:6ika, PDBe:6ika, PDBj:6ika
• PDBsum: 6ika
• PubMed: 30648556
• UniProt: D3XFN7