Structure of PDB 8og4 Chain B Binding Site BS03

Receptor Information
>8og4 Chain B (length=710) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLPIRLLPEKLPPPKATRGCRLHNCFDYSRCPLTSGFPVYVYDSDQFVFG
SYLDPLVKQAFQATARANVYVTENADIACLYVILVGEMQEPVVLRPAELE
KQLYSLPHWRTDGHNHVIINLSRKSDTQNLLYNVSTGRAMVAQSTFYTVQ
YRPGFDLVVSPLVHAMSEPNFMEIPPQVPVKRKYLFTFQGEKIADYDDRI
IATLKAVQDSKLDQVLVEFTCKNQPKPSLPTEWALCGEREDRLELLKLST
FALIITPGDPRLVISSGCATRLFEALEVGAVPVVLGEQVQLPYQDMLQWN
EAALVVPKPRVTEVHFLLRSLSDSDLLAMRRQGRFLWETYFSTADSIFNT
VLAMIRTRIQIPAAPIREEAAAEIPHRSGKETEPPYASPRYLRNFTLTVT
DFYRSWNCAPGPFHLFPHTPFDPVLPSEAKFLGSGTGFRPIGGGAGGSGK
EFQAALGGNVPREQFTVVMLTYEREEVLMNSLERLNGLPYLNKVVVVWNS
PKLPSEDLLWPDIGVPIMVVRTEKNSLNNRFLPWNEIETEAILSIDDDAH
LRHDEIMFGFRVWREARDRIVGFPGRYHAWDIPHQSWLYNSNYSCELSMV
LTGAAFFHKYYAYLYSYVMPQAIRDMVDEYINCEDIAMNFLVSHITRKPP
IKVTSRWTFDDSHFHERHKCINFFVKVYGYMPLLYTQFRVDSVLFKTRLP
HDKTKCFKFI
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain8og4 Chain B Residue 1002 [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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PDB8og4 Molecular mechanism of decision-making in glycosaminoglycan biosynthesis
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L668 Y670 R672 N723 L725 D744 D745 D746
Binding residue
(residue number reindexed from 1)		L470 Y472 R474 N525 L527 D546 D547 D548
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.223: glucuronosyl-galactosyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001888 glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity
GO:0005515 protein binding
GO:0008375 acetylglucosaminyltransferase activity
GO:0016500 protein-hormone receptor activity
GO:0016757 glycosyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0010838 positive regulation of keratinocyte proliferation
GO:0015012 heparan sulfate proteoglycan biosynthetic process
GO:0030307 positive regulation of cell growth
GO:0045617 negative regulation of keratinocyte differentiation
GO:0050728 negative regulation of inflammatory response
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0106015 negative regulation of inflammatory response to wounding
GO:1900016 negative regulation of cytokine production involved in inflammatory response
GO:2000972 positive regulation of detection of glucose
Cellular Component
GO:0005634 nucleus
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8og4, PDBe:8og4, PDBj:8og4
PDBsum8og4
PubMed37828045
UniProtO43909|EXTL3_HUMAN Exostosin-like 3 (Gene Name=EXTL3)

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