Structure of PDB 6k5h Chain C Binding Site BS03

Receptor Information

>6k5h Chain C (length=287) Species: 763924 (Phytophthora capsici LT1534)

AMPTHSDGTVLHLGLRAGQVANRIVSVGSLGRAKVLAQLLDEGHFETFES
ARGFTTYSGKVKGVPVSIVATGMGVPNMDFVVRETRAVVNGPMTIIRFGT
CGAVREEVPPGSVVVNGKGSIMVTRNPDAFFPGASEEDCYRVSRVMPSSS
TLSKALVASMEDKLTALRAEPVIAASSDCDALRVFDGLNATACSFYSSQG
RLDSNFDDRNEKLVEDLTTAHPDLYTVEMETFHLLDLAQRSRGSIQATAA
VLVVANLSGQIVESEVLEALESFWGGVVLQTIVSTPL

Ligand information

• Ligand ID: R1P
• InChI: InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
• InChIKey: YXJDFQJKERBOBM-TXICZTDVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(O1)OP(=O)(O)O)O)O)O
  CACTVS 3.341: OC[C@H]1O[C@H](O[P](O)(O)=O)[C@H](O)[C@@H]1O
  CACTVS 3.341: OC[CH]1O[CH](O[P](O)(O)=O)[CH](O)[CH]1O
  ACDLabs 10.04: O=P(OC1OC(C(O)C1O)CO)(O)O
• Formula: C5 H11 O8 P
• Name: 1-O-phosphono-alpha-D-ribofuranose;
  RIBOSE-1-PHOSPHATE;
  1-O-phosphono-alpha-D-ribose;
  1-O-phosphono-D-ribose;
  1-O-phosphono-ribose
• ChEMBL: CHEMBL603367
• DrugBank: DB03101
• ZINC: ZINC000004228268
• PDB chain: 6k5h Chain C Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k5h Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici.
• Resolution: 2.503 Å
• Binding residue (original residue number in PDB): G35 R39 M80 R104 G106 T107 M236 E237
• Binding residue (residue number reindexed from 1): G28 R32 M73 R97 G99 T100 M229 E230
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.4.2.3: uridine phosphorylase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004850 uridine phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0047847 deoxyuridine phosphorylase activity

Biological Process

• GO:0006218 uridine catabolic process
• GO:0009116 nucleoside metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6k5h, PDBe:6k5h, PDBj:6k5h
• PDBsum: 6k5h
• PubMed: 32493959
• UniProt: A0A410UCT3