Structure of PDB 1pot Chain A Binding Site BS01

Receptor Information
>1pot Chain A (length=322) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDG
AYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDY
SIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQM
ALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNL
GMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLI
NFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGE
WQNDVGAASSIYEEYYQKLKAG
Ligand information
Ligand IDSPD
InChIInChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChIKeyATHGHQPFGPMSJY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CCNCCCN)CN
ACDLabs 10.04NCCCNCCCCN
CACTVS 3.341NCCCCNCCCN
FormulaC7 H19 N3
NameSPERMIDINE;
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;
PA(34)
ChEMBLCHEMBL19612
DrugBankDB03566
ZINCZINC000001532612
PDB chain1pot Chain A Residue 350 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1pot The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		W34 E36 Y37 S83 D168 E171 W255 D257 Y293 Q327
Binding residue
(residue number reindexed from 1)		W9 E11 Y12 S58 D143 E146 W230 D232 Y268 Q302
Annotation score4
Binding affinityMOAD: Kd=3.2uM
PDBbind-CN: -logKd/Ki=5.49,Kd=3.2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0019808 polyamine binding
GO:0019809 spermidine binding
GO:0019810 putrescine binding
Biological Process
GO:0015846 polyamine transport
GO:0015847 putrescine transport
GO:0015848 spermidine transport
GO:1903711 spermidine transmembrane transport
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1pot, PDBe:1pot, PDBj:1pot
PDBsum1pot
PubMed8897598
UniProtP0AFK9|POTD_ECOLI Spermidine/putrescine-binding periplasmic protein (Gene Name=potD)

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