Structure of PDB 6fy4 Chain B Binding Site BS02

Receptor Information
>6fy4 Chain B (length=270) 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
LSVGHHLGKSIPTDNQIKAR
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6fy4 Chain B Residue 301 [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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PDB6fy4 A small molecule chaperone rescues the stability and activity of a cancer-associated variant of NAD(P)H:quinone oxidoreductase 1 in vitro.
Resolution2.76 Å
Binding residue
(original residue number in PDB)		H12 T16 S17 N19 A21 L104 Q105 W106 F107 T148 T149 G150 Y156 I193 R201
Binding residue
(residue number reindexed from 1)		H9 T13 S14 N16 A18 L101 Q102 W103 F104 T145 T146 G147 Y153 I190 R198
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) G150 Y156 H162
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:6fy4, PDBe:6fy4, PDBj:6fy4
PDBsum6fy4
PubMed31605637
UniProtP15559|NQO1_HUMAN NAD(P)H dehydrogenase [quinone] 1 (Gene Name=NQO1)

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