Structure of PDB 7aid Chain C Binding Site BS03

Receptor Information

>7aid Chain C (length=556) Species: 11678 (Human immunodeficiency virus type 1 BH10)

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTN
SQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
DKLVSA

Ligand information

• Ligand ID: REK
• InChI: InChI=1S/C13H19N6O7P/c1-7(3-19-5-17-10-11(14)15-4-16-12(10)19)26-6-27(24,25)18-8(13(22)23)2-9(20)21/h4-5,7-8H,2-3,6H2,1H3,(H,20,21)(H,22,23)(H2,14,15,16)(H2,18,24,25)/t7-,8-/m1/s1
• InChIKey: YBOHKRVDTZQCCV-HTQZYQBOSA-N
• SMILES:
  CACTVS 3.385: C[CH](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)N[CH](CC(O)=O)C(O)=O
  OpenEye OEToolkits 2.0.7: C[C@H](Cn1cnc2c1ncnc2N)OCP(=O)(N[C@H](CC(=O)O)C(=O)O)O
  CACTVS 3.385: C[C@H](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)N[C@H](CC(O)=O)C(O)=O
  OpenEye OEToolkits 2.0.7: CC(Cn1cnc2c1ncnc2N)OCP(=O)(NC(CC(=O)O)C(=O)O)O
• Formula: C13 H19 N6 O7 P
• Name: D-Aspartate Tenofovir;
  (2~{R})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]butanedioic acid
• ChEMBL: CHEMBL4782555
• PDB chain: 7aid Chain C Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7aid Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues.
• Resolution: 3.15 Å
• Binding residue (original residue number in PDB): K65 R72 Y115 Q151 D185
• Binding residue (residue number reindexed from 1): K67 R74 Y117 Q153 D187
• 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:7aid, PDBe:7aid, PDBj:7aid
• PDBsum: 7aid
• PubMed: 33356231
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)