Browse entries in the PDBbind-CN Database

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Related entries of code: 5y59
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
1abtRCSB PDB    PDBbind12-mer
1br8RCSB PDB    PDBbind12-mer
1dkdRCSB PDB    PDBbind12-mer
1gwrRCSB PDB    PDBbind12-mer
1hgtRCSB PDB    PDBbind12-mer
1i8iRCSB PDB    PDBbind12-mer
1jplRCSB PDB    PDBbind12-mer
1jyiRCSB PDB    PDBbind12-mer
1ka7RCSB PDB    PDBbind12-mer
1lf8RCSB PDB    PDBbind12-mer
1mq1RCSB PDB    PDBbind12-mer
1mwnRCSB PDB    PDBbind12-mer
1osgRCSB PDB    PDBbind12-mer
1qweRCSB PDB    PDBbind12-mer
1qwfRCSB PDB    PDBbind12-mer
1shcRCSB PDB    PDBbind12-mer
1ujjRCSB PDB    PDBbind12-mer
1ujkRCSB PDB    PDBbind12-mer
1upkRCSB PDB    PDBbind12-mer
1w80RCSB PDB    PDBbind12-mer
1x8sRCSB PDB    PDBbind12-mer
1xb7RCSB PDB    PDBbind12-mer
1y98RCSB PDB    PDBbind12-mer
2a3iRCSB PDB    PDBbind12-mer
2bypRCSB PDB    PDBbind12-mer
2ci9RCSB PDB    PDBbind12-mer
2fx8RCSB PDB    PDBbind12-mer
2g6qRCSB PDB    PDBbind12-mer
2iv9RCSB PDB    PDBbind12-mer
2jbuRCSB PDB    PDBbind12-mer
2kffRCSB PDB    PDBbind12-mer
2kfgRCSB PDB    PDBbind12-mer
2kfhRCSB PDB    PDBbind12-mer
2ltvRCSB PDB    PDBbind12-mer
2mowRCSB PDB    PDBbind12-mer
2mwpRCSB PDB    PDBbind12-mer
2nczRCSB PDB    PDBbind12-mer
2nwnRCSB PDB    PDBbind12-mer
2ovqRCSB PDB    PDBbind12-mer
2pnxRCSB PDB    PDBbind12-mer
2pv2RCSB PDB    PDBbind12-mer
2pv3RCSB PDB    PDBbind12-mer
2qbxRCSB PDB    PDBbind12-mer
2qicRCSB PDB    PDBbind12-mer
2rolRCSB PDB    PDBbind12-mer
2v85RCSB PDB    PDBbind12-mer
2w10RCSB PDB    PDBbind12-mer
2w85RCSB PDB    PDBbind12-mer
2xzqRCSB PDB    PDBbind12-mer
2y06RCSB PDB    PDBbind12-mer
2y07RCSB PDB    PDBbind12-mer
2y1nRCSB PDB    PDBbind12-mer
2y36RCSB PDB    PDBbind12-mer
2ynrRCSB PDB    PDBbind12-mer
2ynsRCSB PDB    PDBbind12-mer
3c6wRCSB PDB    PDBbind12-mer
3cs8RCSB PDB    PDBbind12-mer
3d32RCSB PDB    PDBbind12-mer
3dowRCSB PDB    PDBbind12-mer
3ds0RCSB PDB    PDBbind12-mer
3ds1RCSB PDB    PDBbind12-mer
3ds3RCSB PDB    PDBbind12-mer
3ds4RCSB PDB    PDBbind12-mer
3eqsRCSB PDB    PDBbind12-mer
3eqyRCSB PDB    PDBbind12-mer
3ggwRCSB PDB    PDBbind12-mer
3hs8RCSB PDB    PDBbind12-mer
3hs9RCSB PDB    PDBbind12-mer
3i5rRCSB PDB    PDBbind12-mer
3iqqRCSB PDB    PDBbind12-mer
3ivqRCSB PDB    PDBbind12-mer
3iwyRCSB PDB    PDBbind12-mer
3jzoRCSB PDB    PDBbind12-mer
3jzpRCSB PDB    PDBbind12-mer
3jzqRCSB PDB    PDBbind12-mer
3jzrRCSB PDB    PDBbind12-mer
3jzsRCSB PDB    PDBbind12-mer
3k26RCSB PDB    PDBbind12-mer
3l3xRCSB PDB    PDBbind12-mer
3l3zRCSB PDB    PDBbind12-mer
3lnjRCSB PDB    PDBbind12-mer
3lnzRCSB PDB    PDBbind12-mer
3mo8RCSB PDB    PDBbind12-mer
3ob1RCSB PDB    PDBbind12-mer
3ob2RCSB PDB    PDBbind12-mer
3poaRCSB PDB    PDBbind12-mer
3shbRCSB PDB    PDBbind12-mer
3sw9RCSB PDB    PDBbind12-mer
3tpxRCSB PDB    PDBbind12-mer
3tszRCSB PDB    PDBbind12-mer
3u2qRCSB PDB    PDBbind12-mer
3uedRCSB PDB    PDBbind12-mer
3uefRCSB PDB    PDBbind12-mer
3ueoRCSB PDB    PDBbind12-mer
3uvwRCSB PDB    PDBbind12-mer
4a4cRCSB PDB    PDBbind12-mer
4b8pRCSB PDB    PDBbind12-mer
4ba3RCSB PDB    PDBbind12-mer
4cc2RCSB PDB    PDBbind12-mer
4cc3RCSB PDB    PDBbind12-mer
4cc7RCSB PDB    PDBbind12-mer
4dowRCSB PDB    PDBbind12-mer
4gaoRCSB PDB    PDBbind12-mer
4gq6RCSB PDB    PDBbind12-mer
4gw1RCSB PDB    PDBbind12-mer
4gw5RCSB PDB    PDBbind12-mer
4hy9RCSB PDB    PDBbind12-mer
4j26RCSB PDB    PDBbind12-mer
4jfxRCSB PDB    PDBbind12-mer
4jfzRCSB PDB    PDBbind12-mer
4jg0RCSB PDB    PDBbind12-mer
4jg1RCSB PDB    PDBbind12-mer
4l58RCSB PDB    PDBbind12-mer
4qh7RCSB PDB    PDBbind12-mer
4rxzRCSB PDB    PDBbind12-mer
4twtRCSB PDB    PDBbind12-mer
4u7tRCSB PDB    PDBbind12-mer
4ux9RCSB PDB    PDBbind12-mer
4w50RCSB PDB    PDBbind12-mer
4whtRCSB PDB    PDBbind12-mer
4whyRCSB PDB    PDBbind12-mer
4x8pRCSB PDB    PDBbind12-mer
4yhzRCSB PDB    PDBbind12-mer
4ym4RCSB PDB    PDBbind12-mer
4z2oRCSB PDB    PDBbind12-mer
4z2pRCSB PDB    PDBbind12-mer
4z68RCSB PDB    PDBbind12-mer
4znxRCSB PDB    PDBbind12-mer
5b56RCSB PDB    PDBbind12-mer
5d2aRCSB PDB    PDBbind12-mer
5eeqRCSB PDB    PDBbind12-mer
5esqRCSB PDB    PDBbind12-mer
5etuRCSB PDB    PDBbind12-mer
5eukRCSB PDB    PDBbind12-mer
5f88RCSB PDB    PDBbind12-mer
5ff6RCSB PDB    PDBbind12-mer
5ggpRCSB PDB    PDBbind12-mer
5gr9RCSB PDB    PDBbind12-mer
5huwRCSB PDB    PDBbind12-mer
5huyRCSB PDB    PDBbind12-mer
5hyqRCSB PDB    PDBbind12-mer
5i2iRCSB PDB    PDBbind12-mer
5icyRCSB PDB    PDBbind12-mer
5iczRCSB PDB    PDBbind12-mer
5id1RCSB PDB    PDBbind12-mer
5ih2RCSB PDB    PDBbind12-mer
5iopRCSB PDB    PDBbind12-mer
5ir1RCSB PDB    PDBbind12-mer
5itfRCSB PDB    PDBbind12-mer
5iv2RCSB PDB    PDBbind12-mer
5ivnRCSB PDB    PDBbind12-mer
5ivzRCSB PDB    PDBbind12-mer
5ixqRCSB PDB    PDBbind12-mer
5iyvRCSB PDB    PDBbind12-mer
5lgrRCSB PDB    PDBbind12-mer
5mocRCSB PDB    PDBbind12-mer
5n7xRCSB PDB    PDBbind12-mer
5n8jRCSB PDB    PDBbind12-mer
5t1kRCSB PDB    PDBbind12-mer
5t1lRCSB PDB    PDBbind12-mer
5t1mRCSB PDB    PDBbind12-mer
5tbnRCSB PDB    PDBbind12-mer
5th2RCSB PDB    PDBbind12-mer
5v1dRCSB PDB    PDBbind12-mer
5w4sRCSB PDB    PDBbind12-mer
5w5sRCSB PDB    PDBbind12-mer
5w5uRCSB PDB    PDBbind12-mer
5w6iRCSB PDB    PDBbind12-mer
5w6rRCSB PDB    PDBbind12-mer
5w6tRCSB PDB    PDBbind12-mer
5w6uRCSB PDB    PDBbind12-mer
5wleRCSB PDB    PDBbind12-mer
5wxfRCSB PDB    PDBbind12-mer
5wxoRCSB PDB    PDBbind12-mer
5xupRCSB PDB    PDBbind12-mer
5xwrRCSB PDB    PDBbind12-mer
5xxkRCSB PDB    PDBbind12-mer
5y1uRCSB PDB    PDBbind12-mer
6bggRCSB PDB    PDBbind12-mer
6e83RCSB PDB    PDBbind12-mer
6f7tRCSB PDB    PDBbind12-mer
6f8gRCSB PDB    PDBbind12-mer
6rr0RCSB PDB    PDBbind12-mer
6qtrRCSB PDB    PDBbind12-mer
6qtoRCSB PDB    PDBbind12-mer
6pitRCSB PDB    PDBbind12-mer
6peuRCSB PDB    PDBbind12-mer
6o3xRCSB PDB    PDBbind12-mer
6nk0RCSB PDB    PDBbind12-mer
6mm5RCSB PDB    PDBbind12-mer
6k5tRCSB PDB    PDBbind12-mer
6k5rRCSB PDB    PDBbind12-mer
6iamRCSB PDB    PDBbind12-mer
6hy2RCSB PDB    PDBbind12-mer
6bykRCSB PDB    PDBbind12-mer
6bw4RCSB PDB    PDBbind12-mer
6bw3RCSB PDB    PDBbind12-mer
6a8gRCSB PDB    PDBbind12-mer
5zopRCSB PDB    PDBbind12-mer
Entry Information
PDB ID5y59
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameATP-dependent DNA helicase II, Ku80
Ligand Name12-mer
EC.Number E.C.3.6.4.12
Resolution 2.4(Å)
Affinity (Kd/Ki/IC50)Kd=5.1uM
Release Year2017
Protein/NA SequenceCheck fasta file
Primary Reference (2018) Cell Vol. 172: pp. 331-343.e13
Ligand Properties
Formula C59H114N18O18
Molecular Weight 1363.650
Exact Mass 1362.860
No. of atoms 209
No. of bonds 208
Polar Surface Area 630.34
LOGP Value -4.47      (Computed with XLOGP3)
-5.21      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 19
No. of Hydrogen Bond Acceptors: 18
No. of Rotatable Bonds: 63
No. of Nitrogen and Oxygen Atoms: 36
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): Q04437  
Entrez Gene IDNCBI Entrez Gene ID: 855132  
ASDInformation of known allosteric effects of PDB entries
 
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