Structure of PDB 6avm Chain C Binding Site BS05

Receptor Information
>6avm Chain C (length=555) Species: 11678 (Human immunodeficiency virus type 1 BH10) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFACKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTD
SQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
DKLVS
Ligand information
Ligand IDD4T
InChIInChI=1S/C10H15N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h2-4,7-8H,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
InChIKeyODSQODTUNULBHF-JGVFFNPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O
FormulaC10 H15 N2 O13 P3
Name2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL485652
DrugBankDB02887
ZINC
PDB chain6avm Chain C Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6avm Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes.
Resolution2.502 Å
Binding residue
(original residue number in PDB)		R72 D110 V111 G112 D113 A114 Y115 D185 K220
Binding residue
(residue number reindexed from 1)		R74 D112 V113 G114 D115 A116 Y117 D187 K222
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6avm, PDBe:6avm, PDBj:6avm
PDBsum6avm
PubMed30499174
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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