Structure of PDB 5jil Chain A Binding Site BS02

Receptor Information

>5jil Chain A (length=369) Species: 31632 (Rat coronavirus)

FNEPLNIVSHLNDDWFLFGDARSDCTYVENNGHPKLDWLDLDPKLCNSGR
ISAKSGNSLFRSFHFTDFYNYSGEGDQVIFYEGVNFSPSHGFKCLANGDN
KIWMGNKARFYARLYEKMAQYRSLSIVTVSYAYGGNAKPTSICKDNKLTL
NNPTFISKESNYADYYYVSEANFTLQGCDEFIVPLCVFNGHSRGSSSDPA
NTYYMDSQMYYNTVTGVFYGFNSTLDVGTTVQNPGLDLTCSYLALSPGNY
KAVSLEFLLSLPSKAICLLKPKRFMPVQVVDSRWNSTRQSDNMTAVACQL
PYCFFRNTSADYSGDTHDVHHGDLYFRQLLSGLLYNVSCIAQQGAFLYNN
VSSIWPVYGYGHCPTAANI

Ligand information

• Ligand ID: 6KL
• InChI: InChI=1S/C14H24N2O9/c1-6(18)15-8-4-14(24-3,13(22)23)25-12(10(8)16-7(2)19)11(21)9(20)5-17/h8-12,17,20-21H,4-5H2,1-3H3,(H,15,18)(H,16,19)(H,22,23)/t8-,9+,10+,11+,12+,14+/m0/s1
• InChIKey: YEXCUFMMPWRNRI-KXEMTNKZSA-N
• SMILES:
  CACTVS 3.385: CO[C]1(C[CH](NC(C)=O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)CO)C(O)=O
  CACTVS 3.385: CO[C@@]1(C[C@H](NC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CO)C(O)=O
  OpenEye OEToolkits 2.0.4: CC(=O)NC1CC(OC(C1NC(=O)C)C(C(CO)O)O)(C(=O)O)OC
  OpenEye OEToolkits 2.0.4: CC(=O)N[C@H]1C[C@@](O[C@H]([C@@H]1NC(=O)C)[C@@H]([C@@H](CO)O)O)(C(=O)O)OC
  ACDLabs 12.01: C(O)(C1(OC)OC(C(C(C1)NC(C)=O)NC(C)=O)C(C(CO)O)O)=O
• Formula: C14 H24 N2 O9
• Name: methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;
  methyl 4,5-bis(acetylamino)-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;
  methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;
  methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid;
  methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-galacto-non-2-ulosidonic acid
• ZINC: ZINC000207905127
• PDB chain: 5jil Chain A Residue 512

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jil Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): A40 Y46 W57 S74 G75 N104 H336 H340
• Binding residue (residue number reindexed from 1): A21 Y27 W38 S55 G56 N85 H317 H321
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.1.1.53: sialate O-acetylesterase.

Gene Ontology

Molecular Function

• GO:0001681 sialate O-acetylesterase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046789 host cell surface receptor binding

Biological Process

• GO:0019064 fusion of virus membrane with host plasma membrane

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:5jil, PDBe:5jil, PDBj:5jil
• PDBsum: 5jil
• PubMed: 27185912
• UniProt: Q3HS77