Structure of PDB 5yun Chain D Binding Site BS01

Receptor Information

>5yun Chain D (length=102) Species: 208964 (Pseudomonas aeruginosa PAO1)

ARGVNKVILVGNVGGDPETRYMPNGNAVTNITLATSESWERTEWHRVVFF
GRLAEIAGEYLRKGSQVYVEGSLRTRKWQGQDGQDRYTTEIVVDINGNMQ
LL

Ligand information

• Ligand ID: MYC
• InChI: InChI=1S/C15H10O8/c16-6-3-7(17)11-10(4-6)23-15(14(22)13(11)21)5-1-8(18)12(20)9(19)2-5/h1-4,16-20,22H
• InChIKey: IKMDFBPHZNJCSN-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=C1c3c(OC(=C1O)c2cc(O)c(O)c(O)c2)cc(O)cc3O
  OpenEye OEToolkits 1.5.0: c1c(cc(c(c1O)O)O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
  CACTVS 3.341: Oc1cc(O)c2C(=O)C(=C(Oc2c1)c3cc(O)c(O)c(O)c3)O
• Formula: C15 H10 O8
• Name: 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE;
  2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE;
  3,3',4',5,5',7-HEXAHYDROXYFLAVONE;
  MYRICETIN;
  CANNABISCETIN
• ChEMBL: CHEMBL164
• DrugBank: DB02375
• ZINC: ZINC000003874317
• PDB chain: 5yun Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yun Crystal structure of SSB complexed with inhibitor myricetin.
• Resolution: 2.67 Å
• Binding residue (original residue number in PDB): I105 N106
• Binding residue (residue number reindexed from 1): I95 N96
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.52,IC50=3uM

Gene Ontology

Molecular Function

• GO:0003697 single-stranded DNA binding

Biological Process

• GO:0006260 DNA replication

External links

• PDB: RCSB:5yun, PDBe:5yun, PDBj:5yun
• PDBsum: 5yun
• PubMed: 30213633
• UniProt: P40947|SSB_PSEAE Single-stranded DNA-binding protein (Gene Name=ssb)