Browse entries in the PDBbind-CN Database

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Related entries of code: 4hdc
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
4gfdRCSB PDB    PDBbind205aa, >4GFD_1|Chains... *
4gsyRCSB PDB    PDBbind205aa, >4GSY_1|Chains... at 100%
4hejRCSB PDB    PDBbind205aa, >4HEJ_1|Chains... at 100%
4hlcRCSB PDB    PDBbind205aa, >4HLC_1|Chains... at 100%
4hldRCSB PDB    PDBbind205aa, >4HLD_1|Chains... at 100%
4qg7RCSB PDB    PDBbind205aa, >4QG7_1|Chains... at 100%
4qgaRCSB PDB    PDBbind205aa, >4QGA_1|Chains... at 100%
4qgfRCSB PDB    PDBbind205aa, >4QGF_1|Chains... at 100%
4qggRCSB PDB    PDBbind205aa, >4QGG_1|Chains... at 100%
4qghRCSB PDB    PDBbind205aa, >4QGH_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 ID4hdc
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameThymidylate kinase
Ligand Name13Y
EC.Number E.C.2.7.4.9
Resolution 2.05(Å)
Affinity (Kd/Ki/IC50)IC50=1.2nM
Release Year2012
Protein/NA SequenceCheck fasta file
Primary Reference (2012) J.Med.Chem. Vol. 55: pp. 10010-10021
Ligand Properties
Formula C28H33ClN3O5
Molecular Weight 527.032
Exact Mass 526.211
No. of atoms 70
No. of bonds 73
Polar Surface Area 105.83
LOGP Value 3.88      (Computed with XLOGP3)
5.57      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 2
No. of Hydrogen Bond Acceptors: 4
No. of Rotatable Bonds: 7
No. of Nitrogen and Oxygen Atoms: 8
No. of Rings: 4
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): P65249  
Entrez Gene IDNo matched NCBI Entrez Gene ID found!
ASDInformation of known allosteric effects of PDB entries
 
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