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Related entries of code: 5nkk
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
No similar entries are found!
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
1d2eRCSB PDB    PDBbindGDP
1darRCSB PDB    PDBbindGDP
1fzqRCSB PDB    PDBbindGDP
1r5nRCSB PDB    PDBbindGDP
1ryfRCSB PDB    PDBbindGDP
1tpzRCSB PDB    PDBbindGDP
1tq4RCSB PDB    PDBbindGDP
1u2rRCSB PDB    PDBbindGDP
2g83RCSB PDB    PDBbindGDP
2gekRCSB PDB    PDBbindGDP
2h5eRCSB PDB    PDBbindGDP
2qm7RCSB PDB    PDBbindGDP
2rcnRCSB PDB    PDBbindGDP
2wibRCSB PDB    PDBbindGDP
2wjgRCSB PDB    PDBbindGDP
2xtoRCSB PDB    PDBbindGDP
2y4kRCSB PDB    PDBbindGDP
2y4lRCSB PDB    PDBbindGDP
3a1sRCSB PDB    PDBbindGDP
3a1tRCSB PDB    PDBbindGDP
3bbfRCSB PDB    PDBbindGDP
3cphRCSB PDB    PDBbindGDP
3cpjRCSB PDB    PDBbindGDP
3d7mRCSB PDB    PDBbindGDP
3lzzRCSB PDB    PDBbindGDP
3okcRCSB PDB    PDBbindGDP
3zy2RCSB PDB    PDBbindGDP
4dcsRCSB PDB    PDBbindGDP
4idoRCSB PDB    PDBbindGDP
4jycRCSB PDB    PDBbindGDP
4kv9RCSB PDB    PDBbindGDP
4lhvRCSB PDB    PDBbindGDP
4li0RCSB PDB    PDBbindGDP
4lpsRCSB PDB    PDBbindGDP
4nonRCSB PDB    PDBbindGDP
4nxvRCSB PDB    PDBbindGDP
4or6RCSB PDB    PDBbindGDP
4p4tRCSB PDB    PDBbindGDP
4pdeRCSB PDB    PDBbindGDP
4q46RCSB PDB    PDBbindGDP
4rcgRCSB PDB    PDBbindGDP
4rd0RCSB PDB    PDBbindGDP
4rd3RCSB PDB    PDBbindGDP
4rd6RCSB PDB    PDBbindGDP
5aqkRCSB PDB    PDBbindGDP
5goeRCSB PDB    PDBbindGDP
5izkRCSB PDB    PDBbindGDP
5m04RCSB PDB    PDBbindGDP
5mi3RCSB PDB    PDBbindGDP
6g0zRCSB PDB    PDBbindGDP
6jfkRCSB PDB    PDBbindGDP
6h4dRCSB PDB    PDBbindGDP
5ymxRCSB PDB    PDBbindGDP
5mi9RCSB PDB    PDBbindGDP
6u9vRCSB PDB    PDBbindGDP
Entry Information
PDB ID5nkk
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein Namecomplex of Protein SMG8c-SMG9c
Ligand NameGDP
EC.Number E.C.-.-.-.-
Resolution 2.64(Å)
Affinity (Kd/Ki/IC50)Kd=10uM
Release Year2017
Protein/NA SequenceCheck fasta file
Primary Reference (2017) RNA Vol. 23: pp. 1028-1034
Ligand Properties
Formula C10H18N5O11P2
Molecular Weight 446.224
Exact Mass 446.048
No. of atoms 46
No. of bonds 48
Polar Surface Area 287.32
LOGP Value -4.43      (Computed with XLOGP3)
-3.33      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 2
No. of Hydrogen Bond Acceptors: 9
No. of Rotatable Bonds: 7
No. of Nitrogen and Oxygen Atoms: 16
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): O62301  Q9XWJ1  
Entrez Gene IDNCBI Entrez Gene ID: 175103  175132  
ASDInformation of known allosteric effects of PDB entries
 
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