Structure of PDB 8d22 Chain A Binding Site BS01

Receptor Information

>8d22 Chain A (length=377) Species: 57270 (Plasmodium falciparum Palo Alto/Uganda)

GPVIGIDLGTTYSCVGVFKNGRVEILNNELGNRITPSYVSFVDGERKVGE
AAKLEATLHPTQTVFDVKRLIGRKFDDQEVVKDRSLLPYEIVNNQGKPNI
KVQIKDKDTTFAPEQISAMVLEKMKEIAQSFLGKPVKNAVVTVPAYFNDA
QRQATKDAGTIAGLNIVRIINEPTAAALAYGLDKKEETSILVYDLGGGTF
DVSILVIDNGVFEVYATAGNTHLGGEDFDQRVMDYFIKMFKKKNNIDLRT
DKRAIQKLRKEVEIAKRNLSVVHSTQIEIEDIVEGHNFSETLTRAKFEEL
NDDLFRETLEPVKKVLDDAKYEKSKIDEIVLVGGSTRIPKIQQIIKEFFN
GKEPNRGINPDEAVAYGAAIQAGIILG

Ligand information

• Ligand ID: Q8L
• InChI: InChI=1S/C18H19IN6O4/c1-20-17(28)14-12(26)13(27)18(29-14)25-8-24-11-15(22-7-23-16(11)25)21-6-9-3-2-4-10(19)5-9/h2-5,7-8,12-14,18,26-27H,6H2,1H3,(H,20,28)(H,21,22,23)/t12-,13+,14-,18+/m0/s1
• InChIKey: HUJXGQILHAUCCV-MOROJQBDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CNC(=O)C1C(C(C(O1)n2cnc3c2ncnc3NCc4cccc(c4)I)O)O
  CACTVS 3.385: CNC(=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCc4cccc(I)c4)ncnc23
  OpenEye OEToolkits 2.0.7: CNC(=O)[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCc4cccc(c4)I)O)O
  CACTVS 3.385: CNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCc4cccc(I)c4)ncnc23
  ACDLabs 12.01: Ic1cccc(c1)CNc1ncnc2c1ncn2C1OC(C(O)C1O)C(=O)NC
• Formula: C18 H19 I N6 O4
• Name: Piclidenoson
• ChEMBL: CHEMBL119709
• DrugBank: DB05511
• ZINC: ZINC000003811810
• PDB chain: 8d22 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8d22 Targeting Plasmodium falciparum GRP78-NBD: nucleoside analogues as agents against the malaria chaperone
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G223 G224 G252 E290 K293 R294 S297 V298 G361 S362 R364 D388
• Binding residue (residue number reindexed from 1): G196 G197 G225 E263 K266 R267 S270 V271 G334 S335 R337 D361
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0140662 ATP-dependent protein folding chaperone

External links

• PDB: RCSB:8d22, PDBe:8d22, PDBj:8d22
• PDBsum: 8d22
• PubMed: 36275624
• UniProt: W4J0F1