Structure of PDB 5xn1 Chain A Binding Site BS02

Receptor Information

>5xn1 Chain A (length=551) Species: 11676 (Human immunodeficiency virus 1)

SPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGP
ENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKQ
KKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPMG
WKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKI
EELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSW
TVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAELE
LAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTG
KYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWW
TEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRETKL
GKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYA
LGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLV
S

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: 5xn1 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xn1 HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.
• Resolution: 2.446 Å
• Binding residue (original residue number in PDB): K65 R72 V111 G112 D113 A114 Y115 M151 G152 M184 D185 K220
• Binding residue (residue number reindexed from 1): K63 R70 V109 G110 D111 A112 Y113 M149 G150 M182 D183 K218
• 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:5xn1, PDBe:5xn1, PDBj:5xn1
• PDBsum: 5xn1
• PubMed: 29374261
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)