Browse entries in the PDBbind-CN Database

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Related entries of code: 5yjo
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
5cclRCSB PDB    PDBbind432aa, >5CCL_1|Chain... *
5ccmRCSB PDB    PDBbind428aa, >5CCM_1|Chain... at 100%
5hi7RCSB PDB    PDBbind432aa, >5HI7_1|Chain... at 99%
6ijlRCSB PDB    PDBbind428aa, >6IJL_1|Chain... at 99%
5v37RCSB PDB    PDBbind428aa, >5V37_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 ID5yjo
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameHistone-lysine N-methyltransferase SMYD3
Ligand Name8W0
EC.Number E.C.-.-.-.-
Resolution 2.14(Å)
Affinity (Kd/Ki/IC50)IC50=67nM
Release Year2018
Protein/NA SequenceCheck fasta file
Primary Reference (2019) Acs Med.Chem.Lett. Vol. 10: pp. 978-984
Ligand Properties
Formula C24H33N4O3
Molecular Weight 425.544
Exact Mass 425.255
No. of atoms 64
No. of bonds 67
Polar Surface Area 90.38
LOGP Value 2.66      (Computed with XLOGP3)
2.15      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 1
No. of Hydrogen Bond Acceptors: 3
No. of Rotatable Bonds: 7
No. of Nitrogen and Oxygen Atoms: 7
No. of Rings: 4
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): Q9H7B4  
Entrez Gene IDNCBI Entrez Gene ID: 64754  
ASDInformation of known allosteric effects of PDB entries
 
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