Structure of PDB 5hlf Chain A Binding Site BS03

Receptor Information
>5hlf Chain A (length=554) 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]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVSA
Ligand information
Ligand ID64A
InChIInChI=1S/C13H16N2O7/c1-6-5-15(13(21)14-10(6)16)7-2-3-8(4-7)22-9(11(17)18)12(19)20/h5,7-9H,2-4H2,1H3,(H,17,18)(H,19,20)(H,14,16,21)/t7-,8+/m1/s1
InChIKeyLBUPGXBDONMGHG-SFYZADRCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([C@@H]2CC[C@@H](C2)OC(C(O)=O)C(O)=O)C(=O)NC1=O
OpenEye OEToolkits 2.0.4CC1=CN(C(=O)NC1=O)C2CCC(C2)OC(C(=O)O)C(=O)O
OpenEye OEToolkits 2.0.4CC1=CN(C(=O)NC1=O)[C@@H]2CC[C@@H](C2)OC(C(=O)O)C(=O)O
CACTVS 3.385CC1=CN([CH]2CC[CH](C2)OC(C(O)=O)C(O)=O)C(=O)NC1=O
ACDLabs 12.01C1(=O)C(C)=CN(C(N1)=O)C2CCC(OC(C(=O)O)C(=O)O)C2
FormulaC13 H16 N2 O7
Name{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid
ChEMBL
DrugBank
ZINCZINC000263620688
PDB chain5hlf Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5hlf Exploring the role of the alpha-carboxyphosphonate moiety in the HIV-RT activity of alpha-carboxy nucleoside phosphonates.
Resolution2.95 Å
Binding residue
(original residue number in PDB)
R72 D113 A114 Y115 D185
Binding residue
(residue number reindexed from 1)
R72 D113 A114 Y115 D185
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:5hlf, PDBe:5hlf, PDBj:5hlf
PDBsum5hlf
PubMed26813581
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]