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Related entries of code: 2xdm
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
2xk1RCSB PDB    PDBbind466aa, >2XK1_1|Chains... at 100%
2xlnRCSB PDB    PDBbind489aa, >2XLN_1|Chains... *
2y4aRCSB PDB    PDBbind466aa, >2Y4A_1|Chains... at 100%
2y55RCSB PDB    PDBbind466aa, >2Y55_1|Chains... at 100%
2y59RCSB PDB    PDBbind466aa, >2Y59_1|Chains... at 100%
3zczRCSB PDB    PDBbind467aa, >3ZCZ_1|Chains... at 100%
3zvtRCSB PDB    PDBbind466aa, >3ZVT_1|Chains... at 100%
3zvwRCSB PDB    PDBbind466aa, >3ZVW_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 ID2xdm
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameActinomadura R39 D-Alanyl-D-Alanine-Carboxypeptidase
Ligand NameBO8
EC.Number E.C.3.4.16.4
Resolution 2.4(Å)
Affinity (Kd/Ki/IC50)Ki=32nM
Release Year2010
Protein/NA SequenceCheck fasta file
Primary Reference (2010) Biochemistry. Vol. 49, pp. 6411-641
Ligand Properties
Formula C9H20BN2O5
Molecular Weight 247.076
Exact Mass 247.147
No. of atoms 37
No. of bonds 36
Polar Surface Area 134.5
LOGP Value -2.79      (Computed with XLOGP3)
-1.43      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 4
No. of Hydrogen Bond Acceptors: 5
No. of Rotatable Bonds: 10
No. of Nitrogen and Oxygen Atoms: 7
No. of Rings: 0
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): P39045  
Entrez Gene IDNo matched NCBI Entrez Gene ID found!
ASDInformation of known allosteric effects of PDB entries

 
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