Structure of PDB 3dsz Chain A Binding Site BS01

Receptor Information
>3dsz Chain A (length=172) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIPAPPLSKVPLQQNFQDNQFHGKWYQVGRAGNAALREDKDPQKMTAQIY
ELKEDKSYNVTAVRFRKKKCDYLTMTFVPGSQPGEFTLGNIKSYPGLTSY
LVRVVSTNYNQHAMVFFKKVSQNREYFSITLLGRTKELASELKENFIRFS
KSLGLPENHIVFPVPIDQCIDG
Ligand information
Ligand IDLIZ
InChIInChI=1S/C30H45N5O13S/c36-16-30(17-37,18-38)32-29(49)31-20-7-5-19(6-8-20)9-21(33(11-24(39)40)12-25(41)42)10-34(13-26(43)44)22-3-1-2-4-23(22)35(14-27(45)46)15-28(47)48/h5-8,21-23,36-38H,1-4,9-18H2,(H,39,40)(H,41,42)(H,43,44)(H,45,46)(H,47,48)(H2,31,32,49)/t21-,22+,23+/m1/s1
InChIKeyZDJITWBUQUCYMP-VJBWXMMDSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04S=C(NC(CO)(CO)CO)Nc1ccc(cc1)CC(N(CC(=O)O)CC(=O)O)CN(CC(=O)O)C2CCCCC2N(CC(=O)O)CC(=O)O
CACTVS 3.341OCC(CO)(CO)NC(=S)Nc1ccc(C[CH](CN(CC(O)=O)[CH]2CCCC[CH]2N(CC(O)=O)CC(O)=O)N(CC(O)=O)CC(O)=O)cc1
CACTVS 3.341OCC(CO)(CO)NC(=S)Nc1ccc(C[C@H](CN(CC(O)=O)[C@H]2CCCC[C@@H]2N(CC(O)=O)CC(O)=O)N(CC(O)=O)CC(O)=O)cc1
OpenEye OEToolkits 1.5.0c1cc(ccc1CC(CN(CC(=O)O)C2CCCCC2N(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O)NC(=S)NC(CO)(CO)CO
OpenEye OEToolkits 1.5.0c1cc(ccc1C[C@H](C[N@](CC(=O)O)[C@H]2CCCC[C@@H]2N(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O)NC(=S)NC(CO)(CO)CO
FormulaC30 H45 N5 O13 S
NameN-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)amino]-3-[4-({[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]carbamothioyl}amino)phenyl]propyl}glycine
ChEMBL
DrugBank
ZINCZINC000058649372
PDB chain3dsz Chain A Residue 187 [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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PDB3dsz High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Q33 R36 T52 Q54 V66 A68 R70 D77 L79 Y106 F123 T136
Binding residue
(residue number reindexed from 1)		Q27 R30 T46 Q48 V60 A62 R64 D71 L73 Y100 F117 T130
Annotation score1
Binding affinityMOAD: Kd=17.1nM
PDBbind-CN: -logKd/Ki=7.77,Kd=17.1nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dsz, PDBe:3dsz, PDBj:3dsz
PDBsum3dsz
PubMed19227970
UniProtP80188|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin (Gene Name=LCN2)

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