Structure of PDB 5tuq Chain A Binding Site BS01

Receptor Information
>5tuq Chain A (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]
VPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAG
LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD
KLVSA
Ligand information
Ligand IDJ63
InChIInChI=1S/C22H30N2O4/c1-16(2)20-19(13-17-9-5-3-6-10-17)23(22(26)24(27)21(20)25)15-28-14-18-11-7-4-8-12-18/h4,7-8,11-12,16-17,27H,3,5-6,9-10,13-15H2,1-2H3
InChIKeyROZLWEMOPMWULZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)C1=C(N(C(=O)N(C1=O)O)COCc2ccccc2)CC3CCCCC3
ACDLabs 12.01O=C3C(=C(CC1CCCCC1)N(COCc2ccccc2)C(N3O)=O)C(C)C
CACTVS 3.385CC(C)C1=C(CC2CCCCC2)N(COCc3ccccc3)C(=O)N(O)C1=O
FormulaC22 H30 N2 O4
Name1-[(benzyloxy)methyl]-6-(cyclohexylmethyl)-3-hydroxy-5-(propan-2-yl)pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL4095043
DrugBank
ZINC
PDB chain5tuq Chain A Residue 601 [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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PDB5tuq 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase.
Resolution2.705 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 V106 Y188 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L101 K102 K104 V107 Y189 F228 W230 L235 H236 P237 Y319
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.35,IC50=0.45uM
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:5tuq, PDBe:5tuq, PDBj:5tuq
PDBsum5tuq
PubMed28182989
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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