Structure of PDB 1rt3 Chain A Binding Site BS01

Receptor Information
>1rt3 Chain A (length=521) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKNSTRWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSIPGIRYQYNVLPQGWKG
SPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEEL
RQHLLRWGLFTPDQKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVN
DIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAE
NREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYA
RMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDAGYVTNRGRQKV
VTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESE
LVNQIIEQLIKKEKVYLAWVP
Ligand information
Ligand IDU05
InChIInChI=1S/C15H14N4O3/c1-3-18-13-9-10(19(21)22)6-7-12(13)17(2)15(20)11-5-4-8-16-14(11)18/h4-9H,3H2,1-2H3
InChIKeyYCFJZPGDTZVVSM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[O-][N+](=O)c2ccc3N(C(=O)c1cccnc1N(c3c2)CC)C
CACTVS 3.341CCN1c2cc(ccc2N(C)C(=O)c3cccnc13)[N+]([O-])=O
OpenEye OEToolkits 1.5.0CCN1c2cc(ccc2N(C(=O)c3c1nccc3)C)[N+](=O)[O-]
FormulaC15 H14 N4 O3
Name6,11-DIHYDRO-11-ETHYL-6-METHYL-9-NITRO-5H-PYRIDO[2,3-B][1,5]BENZODIAZEPIN-5-ONE;
1051U91
ChEMBLCHEMBL71927
DrugBankDB08665
ZINC
PDB chain1rt3 Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rt3 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		P95 L100 Y181 Y188 V189 F227 W229 L234 Y318
Binding residue
(residue number reindexed from 1)		P94 L99 Y176 Y183 V184 F222 W224 L229 Y313
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:1rt3, PDBe:1rt3, PDBj:1rt3
PDBsum1rt3
PubMed9689112
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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