Structure of PDB 6om8 Chain B Binding Site BS01

Receptor Information
>6om8 Chain B (length=463) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVSKVVCVGAGYVGGPTCAMIAHKCPHITVTVVDMNTAKIAEWNSDKLPI
YEPGLDEIVFAARGRNLFFSSDIPKAIAEADLIFISVNTPTKMYGRGKGM
APDLKYVESVSRTIAQYAGGPKIVVEKSTVPVKAAESIGCILREAQKNNE
NLKFQVLSNPEFLAEGTAMKDLANPDRVLIGGESSPEGLQAVAELVRIYE
NWVPRNRIITTNTWSSELSKLVANAFLAQRISSINSISAVCEATGAEISE
VAHAVGYDTRIGSKFLQASVGFGGSCFQKDVLSLVYLCESLNLPQVADYW
QGVININNWQRRRFADKIIAELFNTVTDKKIAIFGFAFKKNTGDTRESSA
IHVIKHLMEEHAKLSVYDPKVQKSQMLNDLASVTSAQDVERLITVESDPY
AAARGAHAIVVLTEWDEFVELNYSQIHNDMQHPAAIFDGRLILDQKALRE
IGFRTFAIGTSPD
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 chain6om8 Chain B Residue 500 [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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PDB6om8 Conservation of Atypical Allostery inC. elegansUDP-Glucose Dehydrogenase.
Resolution2.449 Å
Binding residue
(original residue number in PDB)		G18 Y19 V20 D41 M42 K46 V94 N95 T96 Y113 S135 T136 R353
Binding residue
(residue number reindexed from 1)		G11 Y12 V13 D34 M35 K39 V87 N88 T89 Y106 S128 T129 R346
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T136 E172 K227 N231 C283 D287
Catalytic site (residue number reindexed from 1) T129 E165 K220 N224 C276 D280
Enzyme Commision number 1.1.1.22: UDP-glucose 6-dehydrogenase.
Gene Ontology
Molecular Function
GO:0003979 UDP-glucose 6-dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0051287 NAD binding
Biological Process
GO:0002009 morphogenesis of an epithelium
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006065 UDP-glucuronate biosynthetic process
GO:0009792 embryo development ending in birth or egg hatching
GO:0018991 egg-laying behavior
GO:0022414 reproductive process
GO:0040025 vulval development
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6om8, PDBe:6om8, PDBj:6om8
PDBsum6om8
PubMed31616809
UniProtQ19905|UGDH_CAEEL UDP-glucose 6-dehydrogenase (Gene Name=sqv-4)

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