Browse entries in the PDBbind-CN Database

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Related entries of code: 5db3
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
4gq4RCSB PDB    PDBbind489aa, >4GQ4_1|Chain... *
4og3RCSB PDB    PDBbind480aa, >4OG3_1|Chain... at 100%
4og4RCSB PDB    PDBbind480aa, >4OG4_1|Chain... at 100%
4og5RCSB PDB    PDBbind480aa, >4OG5_1|Chain... at 100%
4og6RCSB PDB    PDBbind489aa, >4OG6_1|Chain... at 99%
4og7RCSB PDB    PDBbind489aa, >4OG7_1|Chain... at 99%
4og8RCSB PDB    PDBbind489aa, >4OG8_1|Chain... at 99%
4x5yRCSB PDB    PDBbind489aa, >4X5Y_1|Chain... at 100%
4x5zRCSB PDB    PDBbind489aa, >4X5Z_1|Chain... at 100%
5db0RCSB PDB    PDBbind489aa, >5DB0_1|Chain... at 100%
5db1RCSB PDB    PDBbind489aa, >5DB1_1|Chain... at 100%
5db2RCSB PDB    PDBbind489aa, >5DB2_1|Chain... at 100%
5dd9RCSB PDB    PDBbind489aa, >5DD9_1|Chain... at 100%
5ddaRCSB PDB    PDBbind489aa, >5DDA_1|Chain... at 100%
5ddbRCSB PDB    PDBbind489aa, >5DDB_1|Chain... at 100%
5ddcRCSB PDB    PDBbind489aa, >5DDC_1|Chain... at 100%
5dddRCSB PDB    PDBbind489aa, >5DDD_1|Chain... at 100%
5ddeRCSB PDB    PDBbind489aa, >5DDE_1|Chain... at 100%
5ddfRCSB PDB    PDBbind489aa, >5DDF_1|Chain... at 100%
6by8RCSB PDB    PDBbind489aa, >6BY8_1|Chain... at 99%
6bxyRCSB PDB    PDBbind489aa, >6BXY_1|Chain... at 100%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
No complexes with the same small molecule ligand are found!
Entry Information
PDB ID5db3
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameMenin
Ligand Name58Q
EC.Number E.C.-.-.-.-
Resolution 1.71(Å)
Affinity (Kd/Ki/IC50)IC50=12nM
Release Year2016
Protein/NA SequenceCheck fasta file
Primary Reference (2016) J.Med.Chem. Vol. 59: pp. 892-913
Ligand Properties
Formula C29H30F3N8OS
Molecular Weight 595.662
Exact Mass 595.222
No. of atoms 72
No. of bonds 77
Polar Surface Area 137.12
LOGP Value 5.72      (Computed with XLOGP3)
6.01      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 3
No. of Hydrogen Bond Acceptors: 4
No. of Rotatable Bonds: 8
No. of Nitrogen and Oxygen Atoms: 9
No. of Rings: 6
Canonical SMILES
InChI String

Links to External Databases
RCSB PDBThe mother database
PDBsumEnhanced annotations on PDB entries
PubchemComprehensive collection of chemical and biological data
UniProtKB ACUniProt accession number (AC): O00255  
Entrez Gene IDNCBI Entrez Gene ID: 4221  
ASDInformation of known allosteric effects of PDB entries
 
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