Structure of PDB 3m8q Chain A Binding Site BS01

Receptor Information
>3m8q 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
GPENPYNTPVFAIKSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIR
Ligand information
Ligand IDDJZ
InChIInChI=1S/C26H29N5O3S/c1-18-14-21(16-27)15-19(2)25(18)34-24-8-11-28-26(30-24)29-22-9-12-31(13-10-22)17-20-4-6-23(7-5-20)35(3,32)33/h4-8,11,14-15,22H,9-10,12-13,17H2,1-3H3,(H,28,29,30)
InChIKeyLPBHCIIMBZNWQE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1cc(cc(c1Oc2ccnc(n2)NC3CCN(CC3)Cc4ccc(cc4)S(=O)(=O)C)C)C#N
ACDLabs 12.01N#Cc4cc(c(Oc1nc(ncc1)NC3CCN(Cc2ccc(cc2)S(=O)(=O)C)CC3)c(c4)C)C
CACTVS 3.370Cc1cc(cc(C)c1Oc2ccnc(NC3CCN(CC3)Cc4ccc(cc4)[S](C)(=O)=O)n2)C#N
FormulaC26 H29 N5 O3 S
Name3,5-dimethyl-4-{[2-({1-[4-(methylsulfonyl)benzyl]piperidin-4-yl}amino)pyrimidin-4-yl]oxy}benzonitrile
ChEMBLCHEMBL1169811
DrugBank
ZINCZINC000043196040
PDB chain3m8q Chain A Residue 562 [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]
PDB3m8q Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-benzyl derivatives with broad potency against resistant mutant viruses.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 K104 S105 V106 V179 Y181 Y188 F227 W229 L234 H235 Y318
Binding residue
(residue number reindexed from 1)		L97 K98 K100 K101 S102 V103 V176 Y178 Y185 F224 W226 L231 H232 Y315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.52,IC50=0.3nM
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:3m8q, PDBe:3m8q, PDBj:3m8q
PDBsum3m8q
PubMed20538456
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]