Structure of PDB 8ej4 Chain B Binding Site BS01

Receptor Information

>8ej4 Chain B (length=850) Species: 9606 (Homo sapiens)

KKDYRKKYRKYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQE
REQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGK
TILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPD
PNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILL
SSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVEILGFSEAKRKEYF
FKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSL
AQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKI
LFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAM
YYLLEELKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEK
KLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQ
RAMDYFPKIEINLSTRMDHMVSSFCIENCHRVESLSLGFLHTSSFCRGLF
SVLSTSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRCGLSH
ECCFDISLVLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWL
VSCCLTSACCQDLASVLSTSHSLTRLYVGENALGDSGVAILCEKAKNPQC
NLQKLGLVNSGLTSVCCSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCE
GLLHPDCKLQVLELDNCNLTSHCCWDLSTLLTSSQSLRKLSLGNNDLGDL
GVMMFCEVLKQQSCLLQNLGLSEMYFNYETKSALETLQEEKPELTVVFEP

Ligand information

• Ligand ID: AGS
• InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
• InChIKey: NLTUCYMLOPLUHL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H16 N5 O12 P3 S
• Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
  ATP-GAMMA-S;
  ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
  ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
  ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL131890
• DrugBank: DB02930
• ZINC: ZINC000008295128
• PDB chain: 8ej4 Chain B Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ej4 Cryo-EM structures of the active NLRP3 inflammasome disc.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R154 Y168 T169 A228 G229 G231 K232 T233 I234 R351 F373 Y381
• Binding residue (residue number reindexed from 1): R22 Y36 T37 A96 G97 G99 K100 T101 I102 R219 F241 Y249
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

External links

• PDB: RCSB:8ej4, PDBe:8ej4, PDBj:8ej4
• PDBsum: 8ej4
• PubMed: 36442502
• UniProt: Q96P20|NLRP3_HUMAN NACHT, LRR and PYD domains-containing protein 3 (Gene Name=NLRP3)