Structure of PDB 1kbq Chain B Binding Site BS02

Receptor Information
>1kbq Chain B (length=271) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRALIVLAHSERTSFNYAMKEAAAAALKKKGWEVVESDLYAMNFNPIISR
KDITGKLKDPANFQYPAESVLAYKEGHLSPDIVAEQKKLEAADLVIFQFP
LQWFGVPAILKGWFERVFIGEFAYTYAAMYDKGPFRSKKAVLSITTGGSG
SMYSLQGIHGDMNVILWPIQSGILHFCGFQVLEPQLTYSIGHTPADARIQ
ILEGWKKRLENIWDETPLYFAPSSLFDLNFQAGFLMKKEVQDEEKNKKFG
LSVGHHLGKSIPTDNQIKARK
Ligand information
Ligand ID936
InChIInChI=1S/C18H16N2O6/c1-10-13(9-26-12-6-4-11(5-7-12)20(23)24)16-17(19(10)2)14(21)8-15(25-3)18(16)22/h4-8H,9H2,1-3H3
InChIKeyIBLWSLZYYZHSRG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2c(n1C)C(=O)C=C(C2=O)OC)COc3ccc(cc3)[N+](=O)[O-]
CACTVS 3.341COC1=CC(=O)c2n(C)c(C)c(COc3ccc(cc3)[N+]([O-])=O)c2C1=O
ACDLabs 10.04[O-][N+](=O)c3ccc(OCc2c1c(C(=O)C=C(OC)C1=O)n(c2C)C)cc3
FormulaC18 H16 N2 O6
Name5-METHOXY-1,2-DIMETHYL-3-(4-NITROPHENOXYMETHYL)INDOLE-4,7-DIONE
ChEMBLCHEMBL357217
DrugBankDB02400
ZINCZINC000000587989
PDB chain1kbq Chain B Residue 704 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kbq Characterization of a mechanism-based inhibitor of NAD(P)H:quinone oxidoreductase 1 by biochemical, X-ray crystallographic, and mass spectrometric approaches.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		P68 Y126 Y128 F178 F232 F236
Binding residue
(residue number reindexed from 1)		P66 Y124 Y126 F176 F230 F234
Annotation score1
Binding affinityMOAD: Ki=0.45uM
BindingDB: Ki=450nM
Enzymatic activity
Catalytic site (original residue number in PDB) G149 Y155 H161
Catalytic site (residue number reindexed from 1) G147 Y153 H159
Enzyme Commision number 1.6.5.2: NAD(P)H dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003955 NAD(P)H dehydrogenase (quinone) activity
GO:0004128 cytochrome-b5 reductase activity, acting on NAD(P)H
GO:0004784 superoxide dismutase activity
GO:0005515 protein binding
GO:0008753 NADPH dehydrogenase (quinone) activity
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
GO:0050136 NADH:ubiquinone reductase (non-electrogenic) activity
Biological Process
GO:0000209 protein polyubiquitination
GO:0002931 response to ischemia
GO:0006116 NADH oxidation
GO:0006743 ubiquinone metabolic process
GO:0006801 superoxide metabolic process
GO:0006805 xenobiotic metabolic process
GO:0006809 nitric oxide biosynthetic process
GO:0006979 response to oxidative stress
GO:0007271 synaptic transmission, cholinergic
GO:0007584 response to nutrient
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0009725 response to hormone
GO:0009743 response to carbohydrate
GO:0014070 response to organic cyclic compound
GO:0014075 response to amine
GO:0019430 removal of superoxide radicals
GO:0030163 protein catabolic process
GO:0032355 response to estradiol
GO:0032496 response to lipopolysaccharide
GO:0033574 response to testosterone
GO:0034599 cellular response to oxidative stress
GO:0042177 negative regulation of protein catabolic process
GO:0042360 vitamin E metabolic process
GO:0042373 vitamin K metabolic process
GO:0043066 negative regulation of apoptotic process
GO:0043279 response to alkaloid
GO:0043525 positive regulation of neuron apoptotic process
GO:0045087 innate immune response
GO:0045454 cell redox homeostasis
GO:0045471 response to ethanol
GO:0051602 response to electrical stimulus
GO:0070301 cellular response to hydrogen peroxide
GO:0070995 NADPH oxidation
GO:0071248 cellular response to metal ion
GO:0110076 negative regulation of ferroptosis
GO:1904772 response to tetrachloromethane
GO:1904844 response to L-glutamine
GO:1904880 response to hydrogen sulfide
GO:1905395 response to flavonoid
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030425 dendrite
GO:0043025 neuronal cell body
GO:0045202 synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kbq, PDBe:1kbq, PDBj:1kbq
PDBsum1kbq
PubMed11735396
UniProtP15559|NQO1_HUMAN NAD(P)H dehydrogenase [quinone] 1 (Gene Name=NQO1)

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