Structure of PDB 6ej7 Chain A Binding Site BS02

Receptor Information
>6ej7 Chain A (length=706) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFC
PLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYH
KDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTY
LQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSH
GRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRR
FVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLR
ITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFE
AVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTL
YHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIK
HHATNLAVSKLETLETWVMPKKVFKIASPDFGRLQFSEVGTDWDAKERLF
RNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTA
EFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPE
EALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALE
GWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVK
PDGRLR
Ligand information
Ligand IDUDX
InChIInChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1
InChIKeyDQQDLYVHOTZLOR-OCIMBMBZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[C@@H]1CO[C@H](O[P@@](O)(=O)O[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]1O
ACDLabs 10.04O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
OpenEye OEToolkits 1.5.0C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)O)O)O
OpenEye OEToolkits 1.5.0C1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O)O)O
CACTVS 3.341O[CH]1CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH]1O
FormulaC14 H22 N2 O16 P2
NameURIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE;
UDP-ALPHA-D-XYLOPYRANOSE
ChEMBL
DrugBankDB01713
ZINCZINC000008551129
PDB chain6ej7 Chain A 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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PDB6ej7 Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V333 V334 H335 T390 W392 D494 W495 S575 R598 K599
Binding residue
(residue number reindexed from 1)		V82 V83 H84 T139 W141 D243 W244 S324 R347 K348
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.2.26: protein xylosyltransferase.
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0030158 protein xylosyltransferase activity
Biological Process
GO:0030166 proteoglycan biosynthetic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ej7, PDBe:6ej7, PDBj:6ej7
PDBsum6ej7
PubMed29681470
UniProtQ86Y38|XYLT1_HUMAN Xylosyltransferase 1 (Gene Name=XYLT1)

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