Structure of PDB 5ndf Chain A Binding Site BS03

Receptor Information
>5ndf Chain A (length=495) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVRWPDFNQEAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHD
QCQRKQWRVDLPATSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILV
DDYSNDPEDGALLGKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLD
SHCECNEHWLEPLLERVAEDRTRVVSPIIDVINMDNFQYVGASADLKGGF
DWNLVFKWDYMTPEQRRSRQGNPVAPIKTPMIAGGLFVMDKFYFEELGKY
DMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPGGSG
TVFARNTRRAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCK
PFKWYLENVYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECH
NAGGNQEWALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQ
IEGNSKLRHVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL
Ligand information
Ligand IDLU2
InChIInChI=1S/C15H10O6/c16-8-4-11(19)15-12(20)6-13(21-14(15)5-8)7-1-2-9(17)10(18)3-7/h1-6,16-19H
InChIKeyIQPNAANSBPBGFQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Oc1cc(O)c2C(=O)C=C(Oc2c1)c3ccc(O)c(O)c3
OpenEye OEToolkits 1.7.6c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O
ACDLabs 12.01O=C1c3c(OC(=C1)c2ccc(O)c(O)c2)cc(O)cc3O
FormulaC15 H10 O6
Name2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one;
Luteolin
ChEMBLCHEMBL151
DrugBankDB15584
ZINCZINC000018185774
PDB chain5ndf Chain A Residue 608 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ndf The small molecule luteolin inhibits N-acetyl-alpha-galactosaminyltransferases and reduces mucin-type O-glycosylation of amyloid precursor protein.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I253 L270 W282 F361
Binding residue
(residue number reindexed from 1)		I179 L196 W208 F287
Annotation score1
Binding affinityMOAD: Ki=1.4uM
PDBbind-CN: -logKd/Ki=5.85,Ki=1.4uM
Enzymatic activity
Enzyme Commision number 2.4.1.41: polypeptide N-acetylgalactosaminyltransferase.
Gene Ontology
Molecular Function
GO:0004653 polypeptide N-acetylgalactosaminyltransferase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0030145 manganese ion binding
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0016266 O-glycan processing
GO:0018242 protein O-linked glycosylation via serine
GO:0018243 protein O-linked glycosylation via threonine
GO:0051604 protein maturation
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane
GO:0032580 Golgi cisterna membrane
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ndf, PDBe:5ndf, PDBj:5ndf
PDBsum5ndf
PubMed29061849
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

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