Browse entries in the PDBbind-CN Database

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Related entries of code: 2v3d
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
2nsxRCSB PDB    PDBbind497aa, >2NSX_1|Chains... at 100%
2v3eRCSB PDB    PDBbind505aa, >2V3E_1|Chains... at 100%
2wcgRCSB PDB    PDBbind505aa, >2WCG_1|Chains... at 100%
2xwdRCSB PDB    PDBbind505aa, >2XWD_1|Chains... at 100%
2xweRCSB PDB    PDBbind505aa, >2XWE_1|Chains... at 100%
3rikRCSB PDB    PDBbind497aa, >3RIK_1|Chains... at 100%
3rilRCSB PDB    PDBbind497aa, >3RIL_1|Chains... at 100%
5lvxRCSB PDB    PDBbind497aa, >5LVX_1|Chains... at 99%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
5iefRCSB PDB    PDBbindNBV

Entry Information
PDB ID2v3d
Complex TypeProtein-Ligand
PDBbind Subsetrefined set
Protein NameGLUCOSYLCERAMIDASE
Ligand NameNBV
EC.Number E.C.3.2.1.45
Resolution 1.96(Å)
Affinity (Kd/Ki/IC50)Ki=116uM
Release Year2007
Protein/NA SequenceCheck fasta file
Primary Reference J.Biol.Chem. 282: 29052; Bioorg. Med. Chem. 14, 7736-7744
Ligand Properties
Formula C10H22NO4
Molecular Weight 220.286
Exact Mass 220.155
No. of atoms 37
No. of bonds 37
Polar Surface Area 85.36
LOGP Value -0.63      (Computed with XLOGP3)
-1.30      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 5
No. of Hydrogen Bond Acceptors: 4
No. of Rotatable Bonds: 8
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): P04062  
Entrez Gene IDNCBI Entrez Gene ID: 2629  
ASDInformation of known allosteric effects of PDB entries

 
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