Structure of PDB 4d0z Chain F Binding Site BS02

Receptor Information
>4d0z Chain F (length=491) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVRWPDFNQEAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHD
QCQRKDLPATSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILVDDYS
NDPEDGALLGKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLDSHCE
CNEHWLEPLLERVAEDRTRVVSPIIDVINMDNFQYVGASADLKGGFDWNL
VFKWDYMTPEQRRSRQGNPVAPIKTPMIAGGLFVMDKFYFEELGKYDMMM
DVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPGGSGTVFA
RNTRRAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKW
YLENVYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGG
NQEWALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQIEGN
SKLRHVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL
Ligand information
Ligand IDHWU
InChIInChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12+,13-,14-,15-,16?/m1/s1
InChIKeyJPRVHSQHWXZSNC-KZEZZKTRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3SC(C(O)C(O)C3NC(=O)C)CO)O)O
CACTVS 3.385CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)S[C@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
CACTVS 3.385CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)S[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.7.6CC(=O)N[C@@H]1[C@H]([C@H]([C@H](S[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
OpenEye OEToolkits 1.7.6CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
FormulaC17 H27 N3 O16 P2 S
Name(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate;
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGALACTOSAMINE
ChEMBL
DrugBank
ZINC
PDB chain4d0z Chain F Residue 1571 [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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PDB4d0z Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
T143 F144 D176 R201 L204 R208 D224 S225 H226 A307 G308 G309 W331 G332 E334 H359 Y367
Binding residue
(residue number reindexed from 1)
T65 F66 D98 R123 L126 R130 D146 S147 H148 A229 G230 G231 W253 G254 E256 H281 Y289
Annotation score2
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:4d0z, PDBe:4d0z, PDBj:4d0z
PDBsum4d0z
PubMed24954443
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

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