Structure of PDB 6c58 Chain D Binding Site BS01

Receptor Information
>6c58 Chain D (length=449) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLP
IYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNDLKYIEACARR
IVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLSNPEFLAE
GTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTNTWS
SELSKLAANLFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKF
LKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFA
SRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSIYISKYLMDEGAHLH
IYDPKVPREQIVVDLSHPVSEDDQVSRLVTISKDPYEACDGAHAVVICTE
WDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKK
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 chain6c58 Chain D Residue 501 [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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PDB6c58 The A225L Substitution of hUGDH alters structure and function
Resolution2.198 Å
Binding residue
(original residue number in PDB)		T131 F162 L163 A164 E165 K220 I231 F265 K267 S269 F272 G273 C276 F277 F338 K339 R442
Binding residue
(residue number reindexed from 1)		T116 F147 L148 A149 E150 K205 I216 F250 K252 S254 F257 G258 C261 F262 F323 K324 R426
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T131 E165 K220 N224 C276 D280
Catalytic site (residue number reindexed from 1) T116 E150 K205 N209 C261 D265
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:0001702 gastrulation with mouth forming second
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006065 UDP-glucuronate biosynthetic process
GO:0015012 heparan sulfate proteoglycan biosynthetic process
GO:0030206 chondroitin sulfate biosynthetic process
GO:0034214 protein hexamerization
GO:0048666 neuron development
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6c58, PDBe:6c58, PDBj:6c58
PDBsum6c58
PubMed
UniProtO60701|UGDH_HUMAN UDP-glucose 6-dehydrogenase (Gene Name=UGDH)

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