Structure of PDB 6zdl Chain AAA Binding Site BS03

Receptor Information

>6zdl Chain AAA (length=359) Species: 9606 (Homo sapiens)

LNNYLHVFYYSWYGNPQFDGKYIHWNHPVLEHWDPRIAKNYPQGRHNPPD
DIGSSFYPELGSYSSRDPSVIETHMRQMRSASIGVLALSWYPPDVNDENG
EPTDNLVPTILDKAHKYNLKVTFHIEPYSNRDDQNMYKNVKYIIDKYGNH
PAFYRYKTKTGNALPMFYVYDSYITKPEKWANLLTTSGSRSIRNSPYDGL
FIALLVEEKHKYDILQSGFDGIYTYFATNGFTYGSSHQNWASLKLFCDKY
NLIFIPSVGPGYIDTSIRPWNTQNTRNRINGKYYEIGLSAALQTRPSLIS
ITSFNEWHEGTQIEKAVPKRTSNTVYLDYRPHKPGLYLELTRKWSEKYSK
ERATYALDR

Ligand information

• Ligand ID: IFM
• InChI: InChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
• InChIKey: QPYJXFZUIJOGNX-HSUXUTPPSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1CNC[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
  ACDLabs 10.04: OC1C(CO)CNCC1O
  CACTVS 3.341: OC[C@H]1CNC[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1C(C(C(CN1)O)O)CO
• Formula: C6 H13 N O3
• Name: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
  Afegostat;
  isofagomine;
  (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
• ChEMBL: CHEMBL206468
• DrugBank: DB04545
• ZINC: ZINC000003813668
• PDB chain: 6zdl Chain AAA Residue 506

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zdl Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): Y108 H222 E224 Y268 Y323 E407
• Binding residue (residue number reindexed from 1): Y10 H124 E126 Y170 Y225 E309
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.130: glycoprotein endo-alpha-1,2-mannosidase.

Gene Ontology

Molecular Function

• GO:0016798 hydrolase activity, acting on glycosyl bonds

External links

• PDB: RCSB:6zdl, PDBe:6zdl, PDBj:6zdl
• PDBsum: 6zdl
• PubMed: 33154157
• UniProt: Q5SRI9|MANEA_HUMAN Glycoprotein endo-alpha-1,2-mannosidase (Gene Name=MANEA)