Structure of PDB 7aif Chain A Binding Site BS05

Receptor Information

>7aif 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: RE5
• InChI: InChI=1S/C14H21N6O7P/c1-8(4-20-6-18-11-12(15)16-5-17-13(11)20)27-7-28(25,26)19-9(14(23)24)2-3-10(21)22/h5-6,8-9H,2-4,7H2,1H3,(H,21,22)(H,23,24)(H2,15,16,17)(H2,19,25,26)/t8-,9+/m1/s1
• InChIKey: CIXAAKVRZFPIJB-BDAKNGLRSA-N
• SMILES:
  CACTVS 3.385: C[CH](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)N[CH](CCC(O)=O)C(O)=O
  OpenEye OEToolkits 2.0.7: CC(Cn1cnc2c1ncnc2N)OCP(=O)(NC(CCC(=O)O)C(=O)O)O
  OpenEye OEToolkits 2.0.7: C[C@H](Cn1cnc2c1ncnc2N)OCP(=O)(N[C@@H](CCC(=O)O)C(=O)O)O
  CACTVS 3.385: C[C@H](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O
• Formula: C14 H21 N6 O7 P
• Name: L-Glutamate Tenofovir;
  (2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]pentanedioic acid
• ChEMBL: CHEMBL4797204
• PDB chain: 7aif Chain A Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7aif Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues.
• Resolution: 2.75 Å
• Binding residue (original residue number in PDB): K65 R72 A114 Y115 D185
• Binding residue (residue number reindexed from 1): K66 R73 A115 Y116 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:7aif, PDBe:7aif, PDBj:7aif
• PDBsum: 7aif
• PubMed: 33356231
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)