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Related entries of code: 2vd7
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
2oq6RCSB PDB    PDBbind381aa, >2OQ6_1|Chains... *
2wwjRCSB PDB    PDBbind348aa, >2WWJ_1|Chains... at 99%
2ybkRCSB PDB    PDBbind381aa, >2YBK_1|Chains... at 100%
3njyRCSB PDB    PDBbind381aa, >3NJY_1|Chains... at 100%
3pdqRCSB PDB    PDBbind381aa, >3PDQ_1|Chains... at 100%
4bisRCSB PDB    PDBbind381aa, >4BIS_1|Chains... at 100%
4uraRCSB PDB    PDBbind360aa, >4URA_1|Chains... at 100%
5anqRCSB PDB    PDBbind359aa, >5ANQ_1|Chains... at 100%
5f2sRCSB PDB    PDBbind360aa, >5F2S_1|Chains... at 100%
5f2wRCSB PDB    PDBbind360aa, >5F2W_1|Chains... at 100%
5f32RCSB PDB    PDBbind360aa, >5F32_1|Chains... at 100%
5f37RCSB PDB    PDBbind360aa, >5F37_1|Chains... at 100%
5f39RCSB PDB    PDBbind360aa, >5F39_1|Chains... at 100%
5f3cRCSB PDB    PDBbind360aa, >5F3C_1|Chains... at 100%
5f3eRCSB PDB    PDBbind360aa, >5F3E_1|Chains... at 100%
5f3gRCSB PDB    PDBbind360aa, >5F3G_1|Chains... at 100%
5f3iRCSB PDB    PDBbind360aa, >5F3I_1|Chains... at 100%
5f5iRCSB PDB    PDBbind363aa, >5F5I_1|Chains... at 100%
5vgiRCSB PDB    PDBbind370aa, >5VGI_1|Chains... at 98%
6h4yRCSB PDB    PDBbind360aa, >6H4Y_1|Chains... at 100%
6h4xRCSB PDB    PDBbind360aa, >6H4X_1|Chains... at 100%
6h4wRCSB PDB    PDBbind360aa, >6H4W_1|Chains... at 100%
6h4vRCSB PDB    PDBbind360aa, >6H4V_1|Chains... at 100%
6h4uRCSB PDB    PDBbind360aa, >6H4U_1|Chains... at 100%
6h4tRCSB PDB    PDBbind360aa, >6H4T_1|Chains... at 100%
6h4sRCSB PDB    PDBbind360aa, >6H4S_1|Chains... at 100%
6h4rRCSB PDB    PDBbind360aa, >6H4R_1|Chains... at 100%
6h4qRCSB PDB    PDBbind360aa, >6H4Q_1|Chains... at 100%
6h4pRCSB PDB    PDBbind360aa, >6H4P_1|Chains... at 100%
6h4oRCSB PDB    PDBbind360aa, >6H4O_1|Chains... at 100%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
2gklRCSB PDB    PDBbindPD2
2w0xRCSB PDB    PDBbindPD2
2w2iRCSB PDB    PDBbindPD2
4ie0RCSB PDB    PDBbindPD2
4nhyRCSB PDB    PDBbindPD2
4nrqRCSB PDB    PDBbindPD2
5a3wRCSB PDB    PDBbindPD2
Entry Information
PDB ID2vd7
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein Namehuman JMJD2A catalytic domain
Ligand NamePD2
EC.Number E.C.1.14.11.-
Resolution 2.25(Å)
Affinity (Kd/Ki/IC50)IC50=4.2uM
Release Year2007
Protein/NA SequenceCheck fasta file
Primary Reference (2010) J. Med. Chem., Vol.53, pp.5629-5638
Ligand Properties
Formula C7H5NO4
Molecular Weight 167.119
Exact Mass 167.022
No. of atoms 17
No. of bonds 17
Polar Surface Area 87.49
LOGP Value 2.11      (Computed with XLOGP3)
0.48      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 0
No. of Hydrogen Bond Acceptors: 5
No. of Rotatable Bonds: 0
No. of Nitrogen and Oxygen Atoms: 5
No. of Rings: 1
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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