Structure of PDB 5y6k Chain A Binding Site BS03

Receptor Information
>5y6k Chain A (length=649) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAI
AANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVK
KDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVAN
FFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDV
AFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVV
ARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGF
LKVPPRMDAKMYLGYEYVTAIRNLREGTCPCKPVKWCALSHHERLKCDEW
SVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVL
AENYNAGYFAIAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLY
NKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYT
GAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTR
KPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNSETKDLL
FRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP
Ligand information
Ligand ID8R6
InChIInChI=1S/C22H25N5O9/c1-12-14-6-5-13(25-26-23)8-17(14)36-22(35)15(12)9-18(28)24-7-3-2-4-16(21(33)34)27(10-19(29)30)11-20(31)32/h5-6,8,16H,2-4,7,9-11H2,1H3,(H,24,28)(H,29,30)(H,31,32)(H,33,34)/t16-/m0/s1
InChIKeyPXHFYCYQDOVEPO-INIZCTEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=C(C(=O)Oc2c1ccc(c2)N=[N+]=[N-])CC(=O)NCCCC[C@@H](C(=O)O)N(CC(=O)O)CC(=O)O
CACTVS 3.385CC1=C(CC(=O)NCCCC[CH](N(CC(O)=O)CC(O)=O)C(O)=O)C(=O)Oc2cc(ccc12)N=[N+]=[N-]
CACTVS 3.385CC1=C(CC(=O)NCCCC[C@H](N(CC(O)=O)CC(O)=O)C(O)=O)C(=O)Oc2cc(ccc12)N=[N+]=[N-]
OpenEye OEToolkits 2.0.6CC1=C(C(=O)Oc2c1ccc(c2)N=[N+]=[N-])CC(=O)NCCCCC(C(=O)O)N(CC(=O)O)CC(=O)O
FormulaC22 H25 N5 O9
Name(2S)-6-[2-(7-azido-4-methyl-2-oxidanylidene-chromen-3-yl)ethanoylamino]-2-[bis(2-hydroxy-2-oxoethyl)amino]hexanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5y6k Chain A Residue 705 [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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PDB5y6k Tracking iron-associated proteomes in pathogens by a fluorescence approach.
Resolution2.86 Å
Binding residue
(original residue number in PDB)		R602 Q603
Binding residue
(residue number reindexed from 1)		R584 Q585
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.07,Kd=0.86uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008198 ferrous iron binding
GO:0008199 ferric iron binding
GO:0019899 enzyme binding
GO:0034986 iron chaperone activity
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
GO:1990459 transferrin receptor binding
Biological Process
GO:0006826 iron ion transport
GO:0006879 intracellular iron ion homeostasis
GO:0007015 actin filament organization
GO:0009617 response to bacterium
GO:0019731 antibacterial humoral response
GO:0030316 osteoclast differentiation
GO:0031647 regulation of protein stability
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0034756 regulation of iron ion transport
GO:0042327 positive regulation of phosphorylation
GO:0045780 positive regulation of bone resorption
GO:0045893 positive regulation of DNA-templated transcription
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0070371 ERK1 and ERK2 cascade
GO:0071281 cellular response to iron ion
GO:2000147 positive regulation of cell motility
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005788 endoplasmic reticulum lumen
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0009925 basal plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030139 endocytic vesicle
GO:0030669 clathrin-coated endocytic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0034774 secretory granule lumen
GO:0045178 basal part of cell
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:1990712 HFE-transferrin receptor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5y6k, PDBe:5y6k, PDBj:5y6k
PDBsum5y6k
PubMed29323384
UniProtP02787|TRFE_HUMAN Serotransferrin (Gene Name=TF)

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