Structure of PDB 6s3x Chain B Binding Site BS01

Receptor Information
>6s3x Chain B (length=474) Species: 1079 (Blastochloris viridis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWPVYHRIDGPIVMIGFGSIGRGTLPLIERHFAFDRSKLVVIDPSDEARK
LAEARGVRFIQQAVTRDNYRELLVPLLTAGPGQGFCVNLSVDTSSLDIME
LARENGALYIDTVVEPWLGFYFDPDLKPEARSNYALRETVLAARRNKPGG
TTAVSCCGANPGMVSWFVKQALVNLAADLGVTGEEPTTREEWARLAMDLG
VKGIHIAQRDTQRASFPKPFDVFVNTWSVEGFVSEGLQPAELGWGTFERW
MPDNARGHDSGCGAGIYLLQPGANTRVRSWTPTAMAQYGFLVTHNESISI
ADFLTVRDAAGQAVYRPTCHYAYHPCNDAVLSLHEMFGSGKRQSDWRILD
ETEIVDGIDELGVLLYGHGKNAYWYGSQLSIEETRRIAPDQNATGLQVSS
AVLAGMVWALENPNAGIVEADDLDFRRCLEVQTPYLGPVVGVYTDWTPLA
GRPGLFPEDIDTSDPWQFRNVLVR
Ligand information
Ligand IDAG2
InChIInChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChIKeyQYPPJABKJHAVHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCCNC(N)=N
ACDLabs 10.04[N@H]=C(N)NCCCCN
OpenEye OEToolkits 1.5.0C(CCNC(=N)N)CN
FormulaC5 H14 N4
NameAGMATINE;
(4-AMINOBUTYL)GUANIDINE
ChEMBLCHEMBL58343
DrugBankDB08838
ZINCZINC000001532560
PDB chain6s3x Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6s3x Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction.
Resolution1.72 Å
Binding residue
(original residue number in PDB)		R146 R191 D424
Binding residue
(residue number reindexed from 1)		R144 R189 D422
Annotation score1
Enzymatic activity
Enzyme Commision number 2.5.1.44: homospermidine synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0047296 homospermidine synthase activity
GO:0050514 homospermidine synthase (spermidine-specific) activity

View graph for
Molecular Function
External links
PDB RCSB:6s3x, PDBe:6s3x, PDBj:6s3x
PDBsum6s3x
PubMed34605434
UniProtO32323|HSS_BLAVI Homospermidine synthase (Gene Name=hss)

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