Structure of PDB 3qip Chain A Binding Site BS03

Receptor Information
>3qip Chain A (length=554) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKK
KKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQG
WKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKI
EELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSW
TVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELE
LAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTG
KYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWW
TEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKL
GKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYA
LGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLV
SAGI
Ligand information
Ligand IDP4Y
InChIInChI=1S/C20H15N3O4/c24-18-17(20(26)27)22-15(23-19(18)25)10-13-12-8-4-5-9-14(12)21-16(13)11-6-2-1-3-7-11/h1-9,21,24H,10H2,(H,26,27)(H,22,23,25)
InChIKeyJONQCFJPPWOWOJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2c(c3ccccc3[nH]2)Cc4nc(c(c(n4)O)O)C(=O)O
CACTVS 3.370OC(=O)c1nc(Cc2c([nH]c3ccccc23)c4ccccc4)nc(O)c1O
ACDLabs 12.01O=C(O)c1nc(nc(O)c1O)Cc3c2ccccc2nc3c4ccccc4
FormulaC20 H15 N3 O4
Name5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000066167058
PDB chain3qip Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qip Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.
Resolution2.0926 Å
Binding residue
(original residue number in PDB)		D443 E478 D498 A538 H539
Binding residue
(residue number reindexed from 1)		D441 E476 D496 A536 H537
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.89,Kd=129nM
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
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Biological Process
External links
PDB RCSB:3qip, PDBe:3qip, PDBj:3qip
PDBsum3qip
PubMed21464257
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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