Structure of PDB 3ped Chain B Binding Site BS01

Receptor Information
>3ped Chain B (length=172) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREKDPQKMYATI
YELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTS
YLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRF
SKSLGLPENHIVFPVPIDQCID
Ligand information
Ligand IDZYF
InChIInChI=1S/C37H53N5O12/c1-25(23-31(44)38-27-16-11-14-22-42(52)36(27)49)54-37(50)28(39-34(48)29-24-53-35(40-29)26-15-9-10-18-30(26)43)17-12-13-21-41(51)32(45)19-7-5-3-2-4-6-8-20-33(46)47/h7,9-10,15,18-19,25,27-29,43,51-52H,2-6,8,11-14,16-17,20-24H2,1H3,(H,38,44)(H,39,48)(H,46,47)/b19-7-/t25-,27-,28-,29-/m0/s1
InChIKeyDRNVRDPDTBNRNR-SFCJKLQFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C[C@@H](CC(=O)N[C@H]1CCCCN(C1=O)O)OC(=O)[C@H](CCCCN(C(=O)/C=C\CCCCCCCC(=O)O)O)NC(=O)[C@@H]2COC(=N2)c3ccccc3O
ACDLabs 12.01O=C(NC(C(=O)OC(C)CC(=O)NC1C(=O)N(O)CCCC1)CCCCN(O)C(=O)\C=C/CCCCCCCC(=O)O)C2N=C(OC2)c3c(O)cccc3
CACTVS 3.370C[CH](CC(=O)N[CH]1CCCCN(O)C1=O)OC(=O)[CH](CCCCN(O)C(=O)C=CCCCCCCCC(O)=O)NC(=O)[CH]2COC(=N2)c3ccccc3O
CACTVS 3.370C[C@@H](CC(=O)N[C@H]1CCCCN(O)C1=O)OC(=O)[C@H](CCCCN(O)C(=O)\C=C/CCCCCCCC(O)=O)NC(=O)[C@@H]2COC(=N2)c3ccccc3O
OpenEye OEToolkits 1.7.0CC(CC(=O)NC1CCCCN(C1=O)O)OC(=O)C(CCCCN(C(=O)C=CCCCCCCCC(=O)O)O)NC(=O)C2COC(=N2)c3ccccc3O
FormulaC37 H53 N5 O12
Name
ChEMBL
DrugBank
ZINCZINC000098209684
PDB chain3ped Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ped Siderocalin Recognitin of Carboxymycobactins: Interference by the immune system in intracellular iron acquisition by Mycobacteria tuberculosis
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y52 T54 W79 R81 K125 Y132 F133 K134 Y138
Binding residue
(residue number reindexed from 1)		Y47 T49 W74 R76 K120 Y127 F128 K129 Y133
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ped, PDBe:3ped, PDBj:3ped
PDBsum3ped
PubMed
UniProtP80188|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin (Gene Name=LCN2)

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