Structure of PDB 5ot8 Chain A Binding Site BS01

Receptor Information
>5ot8 Chain A (length=256) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQA
WDGIIPSLTAGRYDAIMAAMSIQPAREKVIAFSRPYLLTPMTFLTTADSP
LLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQ
MMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMF
GPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFG
YDASPK
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 chain5ot8 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ot8 Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		E36 Y39 W77 A94 A95 S97 R102 M117 Q165 T168 S169 H170 S207
Binding residue
(residue number reindexed from 1)		E10 Y13 W51 A68 A69 S71 R76 M91 Q139 T142 S143 H144 S181
Annotation score1
Binding affinityMOAD: Kd=52uM
PDBbind-CN: -logKd/Ki=4.20,Kd=63.8uM
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:5ot8, PDBe:5ot8, PDBj:5ot8
PDBsum5ot8
PubMed29269740
UniProtP35120|NOCT_AGRFC Nopaline-binding periplasmic protein (Gene Name=nocT)

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