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Related entries of code: 6nm4
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
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Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
No complexes with the same small molecule ligand are found!
Entry Information
PDB ID6nm4
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameHistone-lysine N-methyltransferase PRDM9
Ligand NameKS7
EC.Number E.C.-.-.-.-
Resolution 2.58(Å)
Affinity (Kd/Ki/IC50)Kd=87nM
Release Year2019
Protein/NA SequenceCheck fasta file
Primary Reference (2019) Nat Commun Vol. 10: pp. 5759-5759
Ligand Properties
Formula C25H33N6O3
Molecular Weight 465.568
Exact Mass 465.261
No. of atoms 67
No. of bonds 71
Polar Surface Area 81.19
LOGP Value 3.53      (Computed with XLOGP3)
3.53      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 1
No. of Hydrogen Bond Acceptors: 3
No. of Rotatable Bonds: 5
No. of Nitrogen and Oxygen Atoms: 9
No. of Rings: 5
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): Q9NQV7  
Entrez Gene IDNCBI Entrez Gene ID: 56979  
ASDInformation of known allosteric effects of PDB entries
 
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