Structure of PDB 5org Chain A Binding Site BS01

Receptor Information
>5org Chain A (length=257) Species: 1183423 (Agrobacterium tumefaciens str. B6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEKSITIATEGGYAPWNFSGPGGKLDGFEIDLANALCEKMKAKCQIVAQ
NWDGIMPSLTGKKYDAIMAAMSVTPKRQEVIGFSIPYAAGINGFAVMGDS
KLAEMPGLGETYSLDSQADAAKKAIADISSFLNGTTVGVQGSTTASTFLD
KYFKGSVDIKEYKSVEEHNLDLTSGRLDAVLANATVLAAAIEKPEMKGAK
LVGPLFSGGEFGVVAVGLRKEDTALKADFDAAIKAASEDGTIKTLSLKWF
KVDVTPQ
Ligand information
Ligand ID6DB
InChIInChI=1S/C9H18N4O4/c1-5(7(14)15)13-6(8(16)17)3-2-4-12-9(10)11/h5-6,13H,2-4H2,1H3,(H,14,15)(H,16,17)(H4,10,11,12)/t5-,6+/m1/s1
InChIKeyIMXSCCDUAFEIOE-RITPCOANSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC(C(=O)O)NC(CCCNC(=N)N)C(=O)O
ACDLabs 12.01O=C(O)C(NC(C(O)=O)CCCN\C(=N)N)C
OpenEye OEToolkits 2.0.4[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O
CACTVS 3.385C[C@@H](N[C@@H](CCCNC(N)=N)C(O)=O)C(O)=O
CACTVS 3.385C[CH](N[CH](CCCNC(N)=N)C(O)=O)C(O)=O
FormulaC9 H18 N4 O4
Nameoctopine
ChEMBL
DrugBank
ZINCZINC000001529867
PDB chain5org Chain A Residue 321 [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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PDB5org Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		E30 Y33 W71 A88 A89 M90 S91 R96 N111 Q159 T162 T163 N202
Binding residue
(residue number reindexed from 1)		E11 Y14 W52 A69 A70 M71 S72 R77 N92 Q140 T143 T144 N183
Annotation score1
Binding affinityMOAD: Kd=0.009uM
PDBbind-CN: -logKd/Ki=8.40,Kd=0.004uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0015276 ligand-gated monoatomic ion channel activity
Biological Process
GO:0034220 monoatomic ion transmembrane transport
GO:0071705 nitrogen compound 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:5org, PDBe:5org, PDBj:5org
PDBsum5org
PubMed29269740
UniProtP0A4F8|OCCT_RHIRD Octopine-binding periplasmic protein (Gene Name=occT)

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