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Related entries of code: 5vdp
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
6nfgRCSB PDB    PDBbind362aa, >6NFG_1|Chains... at 99%
6nfoRCSB PDB    PDBbind362aa, >6NFO_1|Chains... at 99%
5v8oRCSB PDB    PDBbind362aa, >5V8O_1|Chains... at 99%
5vdoRCSB PDB    PDBbind363aa, >5VDO_1|Chains... at 99%
5vdqRCSB PDB    PDBbind363aa, >5VDQ_1|Chains... at 99%
5vdrRCSB PDB    PDBbind363aa, >5VDR_1|Chains... at 99%
5vdsRCSB PDB    PDBbind363aa, >5VDS_1|Chains... at 99%
5vdtRCSB PDB    PDBbind363aa, >5VDT_1|Chains... at 99%
5vduRCSB PDB    PDBbind363aa, >5VDU_1|Chains... at 99%
5vdvRCSB PDB    PDBbind363aa, >5VDV_1|Chains... at 99%
5vdwRCSB PDB    PDBbind363aa, >5VDW_1|Chains... at 99%
6naoRCSB PDB    PDBbind362aa, >6NAO_1|Chains... at 99%
6mjuRCSB PDB    PDBbind372aa, >6MJU_1|Chain... *
6mjwRCSB PDB    PDBbind372aa, >6MJW_1|Chain... at 100%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
4ksyRCSB PDB    PDBbind1SY
4lohRCSB PDB    PDBbind1SY
4lojRCSB PDB    PDBbind1SY
6a06RCSB PDB    PDBbind1SY

Entry Information
PDB ID5vdp
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NameCyclic GMP-AMP synthase
Ligand Name1SY
EC.Number E.C.-.-.-.-
Resolution 2.3(Å)
Affinity (Kd/Ki/IC50)Kd=89uM
Release Year2017
Protein/NA SequenceCheck fasta file
Primary Reference (2017) Protein Sci. Vol. 26: pp. 2367-2380
Ligand Properties
Formula C20H27N10O13P2
Molecular Weight 677.435
Exact Mass 677.123
No. of atoms 72
No. of bonds 78
Polar Surface Area 364.4
LOGP Value -4.82      (Computed with XLOGP3)
-2.64      (Computed with Open Babel)
Drug likeness No. of Hydrogen Bond Donors: 3
No. of Hydrogen Bond Acceptors: 11
No. of Rotatable Bonds: 4
No. of Nitrogen and Oxygen Atoms: 23
No. of Rings: 7
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): Q8N884  
Entrez Gene IDNCBI Entrez Gene ID: 115004  
ASDInformation of known allosteric effects of PDB entries

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