Structure of PDB 5fv9 Chain E Binding Site BS03

Receptor Information
>5fv9 Chain E (length=483) 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
DMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKVFARNTRRAAE
VWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKWYLENVYPE
LRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGGNQEWALTK
EKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQIEGNSKLRHVGS
NLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL
Ligand information
Ligand IDY6W
InChIInChI=1S/C18H29N2O13P/c21-6-9-13(24)15(26)12(23)8(32-9)2-1-5-34(29,30)31-7-10-14(25)16(27)17(33-10)20-4-3-11(22)19-18(20)28/h3-4,8-10,12-17,21,23-27H,1-2,5-7H2,(H,29,30)(H,19,22,28)/t8-,9-,10-,12+,13+,14-,15-,16-,17-/m1/s1
InChIKeyPDUJCKZVDKZKPQ-RUIRHDHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(CCCC3C(C(C(C(O3)CO)O)O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CCC[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O
ACDLabs 12.01C1(OC(C(C(C1O)O)O)CO)CCCP(OCC3C(C(C(N2C(=O)NC(C=C2)=O)O3)O)O)(O)=O
CACTVS 3.385OC[C@H]1O[C@H](CCC[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
CACTVS 3.385OC[CH]1O[CH](CCC[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
FormulaC18 H29 N2 O13 P
Name
ChEMBL
DrugBank
ZINCZINC000584905745
PDB chain5fv9 Chain E Residue 1572 [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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PDB5fv9 Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		T143 F144 D176 R201 H226 V330 E334
Binding residue
(residue number reindexed from 1)		T69 F70 D102 R127 H152 V256 E260
Annotation score2
Binding affinityMOAD: Kd=254uM
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
View graph for
Cellular Component
External links
PDB RCSB:5fv9, PDBe:5fv9, PDBj:5fv9
PDBsum5fv9
PubMed27071848
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

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