Structure of PDB 1rt1 Chain A Binding Site BS01

Receptor Information
>1rt1 Chain A (length=539) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH
Ligand information
Ligand IDMKC
InChIInChI=1S/C17H22N2O3/c1-4-22-11-19-14(10-13-8-6-5-7-9-13)15(12(2)3)16(20)18-17(19)21/h5-9,12H,4,10-11H2,1-3H3,(H,18,20,21)
InChIKeyMLILORUFDVLTSP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCOCN1C(=O)NC(=O)C(=C1Cc2ccccc2)C(C)C
OpenEye OEToolkits 1.5.0CCOCN1C(=C(C(=O)NC1=O)C(C)C)Cc2ccccc2
ACDLabs 10.04O=C1C(=C(N(C(=O)N1)COCC)Cc2ccccc2)C(C)C
FormulaC17 H22 N2 O3
Name6-BENZYL-1-ETHOXYMETHYL-5-ISOPROPYL URACIL
ChEMBLCHEMBL35033
DrugBankDB08188
ZINCZINC000001536588
PDB chain1rt1 Chain A Residue 999 [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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PDB1rt1 Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 V106 Y181 Y188 G190 F227 W229 L234 Y318
Binding residue
(residue number reindexed from 1)		L100 K101 K103 V106 Y181 Y188 G190 F227 W229 L234 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,IC50=8nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1rt1, PDBe:1rt1, PDBj:1rt1
PDBsum1rt1
PubMed8648598
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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