Structure of PDB 2e5w Chain A Binding Site BS01

Receptor Information
>2e5w Chain A (length=280) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRDMEFIEWYPRGYGVAFKVKRKILEEQSEYQKIEVYETEGFGKLLAIDG
TVQLVTEGEKSYHEPLVHPAMLAHPNPRRVLIIGGGDGGAIREVLKHEEV
EEVIMVEIDKKVIEISAKYIGIDGGILEKMLSDKHEKGKLIIGDGVKFIE
ENSGFDVIIVDSTDPVGPAEMLFSEEFYKNAYRALNDPGIYVTQAGSVYL
FTDEFLTAYRKMRKVFDKVYYYSFPVIGYASPWAFLVGVKGSIDFMKVDA
EKGKKLGLEYYDPDKHETLFQMPRYIVQML
Ligand information
Ligand IDAG3
InChIInChI=1S/C8H21N5/c9-4-3-6-12-5-1-2-7-13-8(10)11/h12H,1-7,9H2,(H4,10,11,13)
InChIKeyXYCUJKFFVBCJEF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[N@H]=C(N)NCCCCNCCCN
OpenEye OEToolkits 1.5.0[H]N=C(N)NCCCCNCCCN
CACTVS 3.341NCCCNCCCCNC(N)=N
OpenEye OEToolkits 1.5.0[H]/N=C(/N)\NCCCCNCCCN
FormulaC8 H21 N5
Name1-{4-[(3-aminopropyl)amino]butyl}guanidine;
N1-aminopropylagmatine
ChEMBL
DrugBank
ZINC
PDB chain2e5w Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2e5w Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E8 V52 Q53 Y62 H63 D87 D161 S162 D164 Q194 Y229 W233
Binding residue
(residue number reindexed from 1)		E8 V52 Q53 Y62 H63 D87 D161 S162 D164 Q194 Y229 W233
Annotation score2
Enzymatic activity
Enzyme Commision number 2.5.1.16: spermidine synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0008295 spermidine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2e5w, PDBe:2e5w, PDBj:2e5w
PDBsum2e5w
PubMed
UniProtO57950|SPEE_PYRHO Polyamine aminopropyltransferase (Gene Name=speE)

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