Browse entries in the PDBbind-CN Database

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Related entries of code: 4d09
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
3ituRCSB PDB    PDBbind345aa, >3ITU_1|Chains... at 98%
4d08RCSB PDB    PDBbind353aa, >4D08_1|Chains... at 96%
4htxRCSB PDB    PDBbind342aa, >4HTX_1|Chains... at 100%
4jibRCSB PDB    PDBbind345aa, >4JIB_1|Chains... at 98%
5tz3RCSB PDB    PDBbind344aa, >5TZ3_1|Chains... at 99%
5tzaRCSB PDB    PDBbind344aa, >5TZA_1|Chains... at 99%
5tzcRCSB PDB    PDBbind344aa, >5TZC_1|Chains... at 99%
5tzhRCSB PDB    PDBbind344aa, >5TZH_1|Chains... at 99%
5tzwRCSB PDB    PDBbind344aa, >5TZW_1|Chains... at 99%
5tzxRCSB PDB    PDBbind344aa, >5TZX_1|Chains... at 99%
5tzzRCSB PDB    PDBbind344aa, >5TZZ_1|Chains... at 99%
5u00RCSB PDB    PDBbind344aa, >5U00_1|Chains... at 99%
5u7dRCSB PDB    PDBbind345aa, >5U7D_1|Chains... at 98%
5u7iRCSB PDB    PDBbind345aa, >5U7I_1|Chains... at 98%
5u7jRCSB PDB    PDBbind345aa, >5U7J_1|Chains... at 98%
5u7kRCSB PDB    PDBbind345aa, >5U7K_1|Chains... at 98%
5u7lRCSB PDB    PDBbind345aa, >5U7L_1|Chains... at 98%
5vp0RCSB PDB    PDBbind345aa, >5VP0_1|Chains... at 99%
5vp1RCSB PDB    PDBbind345aa, >5VP1_1|Chains... at 99%
5xkmRCSB PDB    PDBbind345aa, >5XKM_1|Chains... at 99%
6b96RCSB PDB    PDBbind373aa, >6B96_1|Chains... *
6b97RCSB PDB    PDBbind373aa, >6B97_1|Chains... at 100%
6b98RCSB PDB    PDBbind373aa, >6B98_1|Chains... at 100%
6c7dRCSB PDB    PDBbind342aa, >6C7D_1|Chains... at 99%
6c7eRCSB PDB    PDBbind342aa, >6C7E_1|Chains... at 99%
6c7fRCSB PDB    PDBbind342aa, >6C7F_1|Chains... at 99%
6c7gRCSB PDB    PDBbind342aa, >6C7G_1|Chains... at 99%
6c7iRCSB PDB    PDBbind342aa, >6C7I_1|Chains... at 99%
6c7jRCSB PDB    PDBbind342aa, >6C7J_1|Chains... at 99%
6cybRCSB PDB    PDBbind373aa, >6CYB_1|Chains... at 100%
6cycRCSB PDB    PDBbind373aa, >6CYC_1|Chains... at 100%
6cydRCSB PDB    PDBbind373aa, >6CYD_1|Chains... 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 ID4d09
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NamePDE2a catalytic domain
Ligand Name788
EC.Number E.C.3.1.4.17
Resolution 2.5(Å)
Affinity (Kd/Ki/IC50)IC50=1.7nM
Release Year2014
Protein/NA SequenceCheck fasta file
Primary Reference (2014) Acs Med.Chem.Lett. Vol. 5: pp. 1049-1053
Ligand Properties
Formula C24H19N5O
Molecular Weight 393.441
Exact Mass 393.159
No. of atoms 49
No. of bonds 53
Polar Surface Area 72.18
LOGP Value 4.36      (Computed with XLOGP3)
4.57      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 1
No. of Hydrogen Bond Acceptors: 4
No. of Rotatable Bonds: 5
No. of Nitrogen and Oxygen Atoms: 6
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): O00408  
Entrez Gene IDNCBI Entrez Gene ID: 5138  
ASDInformation of known allosteric effects of PDB entries
 
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