Browse entries in the PDBbind-CN Database

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Related entries of code: 5var
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
2gfaRCSB PDB    PDBbind119aa, >2GFA_1|Chains... at 98%
2qqsRCSB PDB    PDBbind118aa, >2QQS_1|Chains... at 97%
5d6yRCSB PDB    PDBbind121aa, >5D6Y_1|Chains... *
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
No complexes with the same small molecule ligand are found!

Entry Information
PDB ID5var
Complex TypeProtein-Ligand
PDBbind Subsetrefined set
Protein NameLysine-specific demethylase 4A
Ligand Name92Y
EC.Number E.C.1.14.11.-
Resolution 1.83(Å)
Affinity (Kd/Ki/IC50)Kd=81.7uM
Release Year2018
Protein/NA SequenceCheck fasta file
Primary Reference (2018) Bioorg. Med. Chem. Lett. Vol. 28: pp. 1708-1713
Ligand Properties
Formula C16H24NO
Molecular Weight 246.368
Exact Mass 246.186
No. of atoms 42
No. of bonds 44
Polar Surface Area 24.67
LOGP Value 3.27      (Computed with XLOGP3)
0.86      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 2
No. of Hydrogen Bond Acceptors: 1
No. of Rotatable Bonds: 4
No. of Nitrogen and Oxygen Atoms: 2
No. of Rings: 3
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): O75164  
Entrez Gene IDNCBI Entrez Gene ID: 9682  
ASDInformation of known allosteric effects of PDB entries

 
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