Structure of PDB 7aii Chain A Binding Site BS05

Receptor Information

>7aii Chain A (length=555) Species: 11678 (Human immunodeficiency virus type 1 BH10)

VPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAG
LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTNS
QYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD
KLVSA

Ligand information

• Ligand ID: RFE
• InChI: InChI=1S/C14H23N6O5PS/c1-9(5-20-7-18-11-12(15)16-6-17-13(11)20)25-8-26(23,24)19-10(14(21)22)3-4-27-2/h6-7,9-10H,3-5,8H2,1-2H3,(H,21,22)(H2,15,16,17)(H2,19,23,24)/t9-,10+/m1/s1
• InChIKey: PEQPYHOXTFLJCT-ZJUUUORDSA-N
• SMILES:
  CACTVS 3.385: CSCC[CH](N[P](O)(=O)CO[CH](C)Cn1cnc2c(N)ncnc12)C(O)=O
  OpenEye OEToolkits 2.0.7: C[C@H](Cn1cnc2c1ncnc2N)OCP(=O)(N[C@@H](CCSC)C(=O)O)O
  CACTVS 3.385: CSCC[C@H](N[P](O)(=O)CO[C@H](C)Cn1cnc2c(N)ncnc12)C(O)=O
  OpenEye OEToolkits 2.0.7: CC(Cn1cnc2c1ncnc2N)OCP(=O)(NC(CCSC)C(=O)O)O
• Formula: C14 H23 N6 O5 P S
• Name: L-Methionine Tenofovir;
  (2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]-4-methylsulfanyl-butanoic acid
• ChEMBL: CHEMBL4786103
• PDB chain: 7aii Chain A Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7aii Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues.
• Resolution: 2.62 Å
• Binding residue (original residue number in PDB): K65 K66 R72 V111 A114 Y115 Q151 D185
• Binding residue (residue number reindexed from 1): K66 K67 R73 V112 A115 Y116 Q152 D186
• 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:7aii, PDBe:7aii, PDBj:7aii
• PDBsum: 7aii
• PubMed: 33356231
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)