Structure of PDB 4k19 Chain A Binding Site BS01

Receptor Information
>4k19 Chain A (length=174) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYAT
IYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLT
SYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIR
FSKSLGLPENHIVFPVPIDQCIDG
Ligand information
Ligand ID1OD
InChIInChI=1S/C31H34N4O10/c1-17-24(34-30(45-17)20-9-4-12-23(38)27(20)41)31(44)35(15-5-13-32-28(42)18-7-2-10-21(36)25(18)39)16-6-14-33-29(43)19-8-3-11-22(37)26(19)40/h2-4,7-12,17,24,36-41H,5-6,13-16H2,1H3,(H,32,42)(H,33,43)/t17-,24+/m1/s1
InChIKeyLHJFXHHBUCCXIF-OSPHWJPCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(N(CCCNC(=O)c1cccc(O)c1O)CCCNC(=O)c2cccc(O)c2O)C3N=C(OC3C)c4cccc(O)c4O
OpenEye OEToolkits 1.7.6C[C@@H]1[C@H](N=C(O1)c2cccc(c2O)O)C(=O)N(CCCNC(=O)c3cccc(c3O)O)CCCNC(=O)c4cccc(c4O)O
CACTVS 3.370C[C@H]1OC(=N[C@@H]1C(=O)N(CCCNC(=O)c2cccc(O)c2O)CCCNC(=O)c3cccc(O)c3O)c4cccc(O)c4O
OpenEye OEToolkits 1.7.6CC1C(N=C(O1)c2cccc(c2O)O)C(=O)N(CCCNC(=O)c3cccc(c3O)O)CCCNC(=O)c4cccc(c4O)O
CACTVS 3.370C[CH]1OC(=N[CH]1C(=O)N(CCCNC(=O)c2cccc(O)c2O)CCCNC(=O)c3cccc(O)c3O)c4cccc(O)c4O
FormulaC31 H34 N4 O10
Name(4S,5R)-N,N-bis{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide;
fluvibactin
ChEMBL
DrugBank
ZINCZINC000003936138
PDB chain4k19 Chain A Residue 206 [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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PDB4k19 Siderocalin Outwits the Coordination Chemistry of Vibriobactin, a Siderophore of Vibrio cholerae.
Resolution2.74 Å
Binding residue
(original residue number in PDB)		S68 W79 L94 Y100 L103 Y106 K125 K134
Binding residue
(residue number reindexed from 1)		S64 W75 L90 Y96 L99 Y102 K121 K130
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.36,Kd=4.4nM
BindingDB: Kd=34nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0140315 iron ion sequestering activity
GO:1903981 enterobactin binding
Biological Process
GO:0006826 iron ion transport
GO:0006915 apoptotic process
GO:0015891 siderophore transport
GO:0042742 defense response to bacterium
GO:0045087 innate immune response
GO:0120162 positive regulation of cold-induced thermogenesis
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031410 cytoplasmic vesicle
GO:0035580 specific granule lumen
GO:0060205 cytoplasmic vesicle lumen
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4k19, PDBe:4k19, PDBj:4k19
PDBsum4k19
PubMed23755875
UniProtP80188|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin (Gene Name=LCN2)

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