Structure of PDB 8vz9 Chain A Binding Site BS01

Receptor Information

>8vz9 Chain A (length=265) Species: 10090 (Mus musculus)

RTHSLRYFRLAVSDPGPVVPEFISVGYVDSHPITTYDSVTRQKEPKAPWM
AENLAPDHWERYTQLLRGWQQTFKAELRHLQRHYNHSGLHTYQRMIGCEL
LEDGSTTGFLQYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHEL
QYQKNWLEEECIAWLKRFLEYGRDTLERTEHPVVRTTRKETFTTFFCRAH
GFYPPEISMTWMKNGEEIAQEVDYGGVLPSGDGTYQTWLSVNLDPQSVYS
CHVEHSGRQMVLEAP

Ligand information

• Ligand ID: 2LJ
• InChI: InChI=1S/C12H20N4O6/c1-2-3-13-8-10(15-12(22)16-11(8)21)14-4-6(18)9(20)7(19)5-17/h3,6-7,9,17-20H,2,4-5H2,1H3,(H3,14,15,16,21,22)/b13-3+/t6-,7+,9-/m0/s1
• InChIKey: YCMPUNANLDFPQG-FHZGFTDOSA-N
• SMILES:
  CACTVS 3.385: CCC=NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O
  OpenEye OEToolkits 2.0.6: CC/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O
  CACTVS 3.385: CCC=NC1=C(NC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O
  ACDLabs 12.01: C1(=O)NC(NC(=C1\N=C\CC)NCC(O)C(O)C(O)CO)=O
  OpenEye OEToolkits 2.0.6: CCC=NC1=C(NC(=O)NC1=O)NCC(C(C(CO)O)O)O
• Formula: C12 H20 N4 O6
• Name: 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol;
  5-(2-oxopropylideneamino)-6-D-ribitylaminouracil
• PDB chain: 8vz9 Chain A Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vz9 Mouse mucosal-associated invariant T cell receptor recognition of MR1 presenting the vitamin B metabolite, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): Y7 R9 S24 K43 Y62 L66 R94 I96 Y152 W156
• Binding residue (residue number reindexed from 1): Y7 R9 S24 K43 Y62 L66 R94 I96 Y152 W156
• Annotation score: 1

External links

• PDB: RCSB:8vz9, PDBe:8vz9, PDBj:8vz9
• PDBsum: 8vz9
• PubMed: 38537698
• UniProt: Q8HWB0|HMR1_MOUSE Major histocompatibility complex class I-related gene protein (Gene Name=Mr1)