Structure of PDB 3qin Chain A Binding Site BS03

Receptor Information
>3qin Chain A (length=137) Species: 11706,83333 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
KTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKVKNVDLVNQII
EQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV
Ligand information
Ligand IDP1Y
InChIInChI=1S/C13H11BrN2O5/c1-21-8-3-2-6(4-7(8)14)5-9-15-10(13(19)20)11(17)12(18)16-9/h2-4,17H,5H2,1H3,(H,19,20)(H,15,16,18)
InChIKeyLQQYBZYFFRDXNT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0COc1ccc(cc1Br)Cc2nc(c(c(n2)O)O)C(=O)O
ACDLabs 12.01O=C(O)c1nc(nc(O)c1O)Cc2cc(Br)c(OC)cc2
CACTVS 3.370COc1ccc(Cc2nc(O)c(O)c(n2)C(O)=O)cc1Br
FormulaC13 H11 Br N2 O5
Name2-(3-bromo-4-methoxybenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid
ChEMBLCHEMBL572124
DrugBank
ZINCZINC000043022979
PDB chain3qin Chain A Residue 700 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qin Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.
Resolution1.6967 Å
Binding residue
(original residue number in PDB)		D443 E478 D498 A538 H539
Binding residue
(residue number reindexed from 1)		D18 E53 D73 A116 H117
Annotation score1
Binding affinityMOAD: Kd=136nM
PDBbind-CN: -logKd/Ki=6.87,Kd=136nM
Enzymatic activity
Catalytic site (original residue number in PDB) D443 G444 E478 D498 H539 D549
Catalytic site (residue number reindexed from 1) D18 G19 E53 D73 H117 D127
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.
3.1.26.4: ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004523 RNA-DNA hybrid ribonuclease activity

View graph for
Molecular Function
External links
PDB RCSB:3qin, PDBe:3qin, PDBj:3qin
PDBsum3qin
PubMed21464257
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol);
P0A7Y4|RNH_ECOLI Ribonuclease HI (Gene Name=rnhA)

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