Browse entries in the PDBbind-CN Database

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Related entries of code: 3pd2
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
3pd3RCSB PDB    PDBbind147aa, >3PD3_1|Chains... at 100%
3pd4RCSB PDB    PDBbind147aa, >3PD4_1|Chains... at 100%
4rrqRCSB PDB    PDBbind147aa, >4RRQ_1|Chains... at 99%
4rrrRCSB PDB    PDBbind147aa, >4RRR_1|Chains... at 99%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
4rr6RCSB PDB    PDBbindA3S
4rrfRCSB PDB    PDBbindA3S
4rrqRCSB PDB    PDBbindA3S
Entry Information
PDB ID3pd2
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameThreonyl-tRNA synthetase(Pab-NTD)
Ligand NameA3S
EC.Number E.C.6.1.1.3
Resolution 1.86(Å)
Affinity (Kd/Ki/IC50)Kd=3.4uM
Release Year2010
Protein/NA SequenceCheck fasta file
Primary Reference (2010) Proc.Natl.Acad.Sci.USA. Vol. 107:pp. 22117-22121
Ligand Properties
Formula C13H20N7O5
Molecular Weight 354.342
Exact Mass 354.153
No. of atoms 45
No. of bonds 47
Polar Surface Area 196.28
LOGP Value -3.47      (Computed with XLOGP3)
-3.28      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 6
No. of Hydrogen Bond Acceptors: 7
No. of Rotatable Bonds: 9
No. of Nitrogen and Oxygen Atoms: 12
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): Q9UZ14  
Entrez Gene IDNCBI Entrez Gene ID: 1496731  
ASDInformation of known allosteric effects of PDB entries
 
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