Structure of PDB 6npy Chain A Binding Site BS01

Receptor Information
>6npy Chain A (length=798) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IYCAKYRAYVRSRFQCIESLNKRYTRLRLIKEHRIKMELLFDPDDEHSEP
VHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVT
QRSLGDLIMSCCPDPNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPL
CTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHV
EILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIV
CTGLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGLCAHLWGLCSLA
ADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHM
TFQEFFAAMYYLLENVPGSRLKLPSRENYGKFEKGYLIFVVRFLFGLVNQ
ERTAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEIGFLHNMP
KEEEEEEKEGRHLDMVQCVLPSSSHAACSHGLVNSHLTSSFCRGLFSVLS
TSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRCGLSHECCF
DISLVLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWLVSCC
LTSACCQDLASVLSTSHSLTRLYVGENALGDSGVAILCEKAKNPQCNLQK
LGLVNSGLTSVCCSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCEGLLH
PDCKLQVLELDNCNLTSHCCWDLSTLLTSSQSLRKLSLGNNDLGDLGVMM
FCEVLKQQSCLLQNLGLSEMYFNYETKSALETLQEEKPELTVVFEPSW
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6npy Chain A Residue 1101 [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]
PDB6npy Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		R165 Y166 T167 G229 K230 T231 I232 Y379 L411 W414 H520
Binding residue
(residue number reindexed from 1)		R23 Y24 T25 G63 K64 T65 I66 Y213 L245 W248 H349
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0030674 protein-macromolecule adaptor activity
GO:0035591 signaling adaptor activity
GO:0042802 identical protein binding
GO:0042834 peptidoglycan binding
GO:0043531 ADP binding
GO:0043565 sequence-specific DNA binding
GO:0060090 molecular adaptor activity
GO:0070273 phosphatidylinositol-4-phosphate binding
GO:0140297 DNA-binding transcription factor binding
GO:0140299 molecular sensor activity
GO:0140608 cysteine-type endopeptidase activator activity
GO:0140693 molecular condensate scaffold activity
GO:1901981 phosphatidylinositol phosphate binding
Biological Process
GO:0002221 pattern recognition receptor signaling pathway
GO:0002674 negative regulation of acute inflammatory response
GO:0002830 positive regulation of type 2 immune response
GO:0006915 apoptotic process
GO:0006952 defense response
GO:0006954 inflammatory response
GO:0007165 signal transduction
GO:0007231 osmosensory signaling pathway
GO:0009595 detection of biotic stimulus
GO:0032691 negative regulation of interleukin-1 beta production
GO:0032731 positive regulation of interleukin-1 beta production
GO:0032753 positive regulation of interleukin-4 production
GO:0044546 NLRP3 inflammasome complex assembly
GO:0045087 innate immune response
GO:0045630 positive regulation of T-helper 2 cell differentiation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050728 negative regulation of inflammatory response
GO:0050729 positive regulation of inflammatory response
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0051260 protein homooligomerization
GO:0051604 protein maturation
GO:0070269 pyroptotic inflammatory response
GO:0071222 cellular response to lipopolysaccharide
GO:0098586 cellular response to virus
GO:1901223 negative regulation of non-canonical NF-kappaB signal transduction
GO:1901224 positive regulation of non-canonical NF-kappaB signal transduction
GO:2000553 positive regulation of T-helper 2 cell cytokine production
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0031021 interphase microtubule organizing center
GO:0061702 canonical inflammasome complex
GO:0072559 NLRP3 inflammasome complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6npy, PDBe:6npy, PDBj:6npy
PDBsum6npy
PubMed31189953
UniProtQ96P20|NLRP3_HUMAN NACHT, LRR and PYD domains-containing protein 3 (Gene Name=NLRP3)

[Back to BioLiP]