Structure of PDB 4gr9 Chain B Binding Site BS01

Receptor Information
>4gr9 Chain B (length=230) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNFEPRA
TDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQ
FPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGG
TAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEER
KGMVAAWSQRLQTIWKEEPIPCTAHWHFGQ
Ligand information
Ligand ID372
InChIInChI=1S/C13H13N3O2/c1-8(17)15-9-3-4-12-11(7-9)10(5-6-14)13(18)16(12)2/h3-4,7,10H,5H2,1-2H3,(H,15,17)/t10-/m1/s1
InChIKeyPFJVUECMVVMLTI-SNVBAGLBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1cc2c(cc1)N(C(=O)C2CC#N)C)C
CACTVS 3.370CN1C(=O)[CH](CC#N)c2cc(NC(C)=O)ccc12
OpenEye OEToolkits 1.7.6CC(=O)Nc1ccc2c(c1)C(C(=O)N2C)CC#N
OpenEye OEToolkits 1.7.6CC(=O)Nc1ccc2c(c1)[C@H](C(=O)N2C)CC#N
CACTVS 3.370CN1C(=O)[C@H](CC#N)c2cc(NC(C)=O)ccc12
FormulaC13 H13 N3 O2
NameN-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide
ChEMBL
DrugBank
ZINCZINC000101597983
PDB chain4gr9 Chain A Residue 303 [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]
PDB4gr9 Synthesis of novel МТ3 receptor ligands via an unusual Knoevenagel condensation.
Resolution2.291 Å
Binding residue
(original residue number in PDB)		W105 G149 N161
Binding residue
(residue number reindexed from 1)		W105 G149 N161
Annotation score1
Binding affinityMOAD: ic50=7uM
BindingDB: IC50=7000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G149 Y155 N161
Catalytic site (residue number reindexed from 1) G149 Y155 N161
Enzyme Commision number 1.10.5.1: ribosyldihydronicotinamide dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0001512 dihydronicotinamide riboside quinone reductase activity
GO:0003955 NAD(P)H dehydrogenase (quinone) activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors
GO:0031404 chloride ion binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0071949 FAD binding
GO:1904408 melatonin binding
GO:1905594 resveratrol binding
Biological Process
GO:1901662 quinone catabolic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4gr9, PDBe:4gr9, PDBj:4gr9
PDBsum4gr9
PubMed23131339
UniProtP16083|NQO2_HUMAN Ribosyldihydronicotinamide dehydrogenase [quinone] (Gene Name=NQO2)

[Back to BioLiP]