Structure of PDB 1rt2 Chain A Binding Site BS01

Receptor Information
>1rt2 Chain A (length=543) 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
YALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIG
Ligand information
Ligand IDTNK
InChIInChI=1S/C22H24N2O3/c1-16(2)20-19(13-17-9-5-3-6-10-17)24(22(26)23-21(20)25)15-27-14-18-11-7-4-8-12-18/h3-12,16H,13-15H2,1-2H3,(H,23,25,26)
InChIKeyKSAAUHMSLCPIEX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)C1=C(Cc2ccccc2)N(COCc3ccccc3)C(=O)NC1=O
ACDLabs 10.04O=C1C(=C(N(C(=O)N1)COCc2ccccc2)Cc3ccccc3)C(C)C
OpenEye OEToolkits 1.5.0CC(C)C1=C(N(C(=O)NC1=O)COCc2ccccc2)Cc3ccccc3
FormulaC22 H24 N2 O3
Name6-BENZYL-1-BENZYLOXYMETHYL-5-ISOPROPYL URACIL
ChEMBLCHEMBL436546
DrugBankDB08634
ZINCZINC000003580965
PDB chain1rt2 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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PDB1rt2 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 F227 W229 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L100 K101 K103 V106 Y181 Y188 F227 W229 H235 P236 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,IC50=6nM
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:1rt2, PDBe:1rt2, PDBj:1rt2
PDBsum1rt2
PubMed8648598
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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