Structure of PDB 4ncg Chain A Binding Site BS01

Receptor Information
>4ncg Chain A (length=553) 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
GPENPYNTPVFAIKKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGI
Ligand information
Ligand ID2KW
InChIInChI=1S/C17H11ClF3N5O3/c1-25-13(23-24-16(25)28)8-26-3-2-12(17(19,20)21)14(15(26)27)29-11-5-9(7-22)4-10(18)6-11/h2-6H,8H2,1H3,(H,24,28)
InChIKeyZIAOVIPSKUPPQW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)NN=C1CN2C=CC(=C(Oc3cc(Cl)cc(c3)C#N)C2=O)C(F)(F)F
ACDLabs 12.01FC(F)(F)C2=C(Oc1cc(C#N)cc(Cl)c1)C(=O)N(C=C2)CC3=NNC(=O)N3C
OpenEye OEToolkits 1.7.6CN1C(=NNC1=O)CN2C=CC(=C(C2=O)Oc3cc(cc(c3)Cl)C#N)C(F)(F)F
FormulaC17 H11 Cl F3 N5 O3
Name3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile;
Doravirine
ChEMBLCHEMBL2364608
DrugBankDB12301
ZINCZINC000072317283
PDB chain4ncg 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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PDB4ncg Discovery of MK-1439, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against a wide range of resistant mutant HIV viruses.
Resolution2.58 Å
Binding residue
(original residue number in PDB)		L100 K103 V106 V179 Y181 Y188 V189 G190 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L97 K100 V103 V176 Y178 Y185 V186 G187 W226 L231 H232 P233 Y315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.96,IC50=0.011uM
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:4ncg, PDBe:4ncg, PDBj:4ncg
PDBsum4ncg
PubMed24412110
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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