Browse entries in the PDBbind-CN Database

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Related entries of code: 6pyd
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
1a4kRCSB PDB    PDBbind217aa, >1A4K_1|Chains... at 90%
1fl6RCSB PDB    PDBbind217aa, >1FL6_1|Chains... at 93%
4yhmRCSB PDB    PDBbind219aa, >4YHM_2|Chain... *
5tkjRCSB PDB    PDBbind219aa, >5TKJ_2|Chains... at 92%
6cdmRCSB PDB    PDBbind219aa, >6CDM_2|Chains... at 92%
6cdoRCSB PDB    PDBbind219aa, >6CDO_2|Chain... at 92%
6cdpRCSB PDB    PDBbind219aa, >6CDP_2|Chain... at 90%
6ddvRCSB PDB    PDBbind219aa, >6DDV_3|Chain... at 92%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
6pycRCSB PDB    PDBbindP4S

Entry Information
PDB ID6pyd
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein Name3E9 antibody Fab
Ligand NameP4S
EC.Number E.C.-.-.-.-
Resolution 2(Å)
Affinity (Kd/Ki/IC50)Kd=156nM
Release Year2019
Protein/NA SequenceCheck fasta file
Primary Reference (2020) Proc.Natl.Acad.Sci.USA Vol. 117: pp. 292-299
Ligand Properties
Formula C24H32O5
Molecular Weight 400.508
Exact Mass 400.225
No. of atoms 61
No. of bonds 66
Polar Surface Area 83.2
LOGP Value 2.50      (Computed with XLOGP3)
3.37      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 2
No. of Hydrogen Bond Acceptors: 3
No. of Rotatable Bonds: 3
No. of Nitrogen and Oxygen Atoms: 5
No. of Rings: 6
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 ACNo matched UniProt accession number (AC) found!
Entrez Gene IDNo matched NCBI Entrez Gene ID found!
ASDInformation of known allosteric effects of PDB entries

 
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