Structure of PDB 6c58 Chain F Binding Site BS01

Receptor Information
>6c58 Chain F (length=459) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLP
IYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMGKG
RAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPN
LNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEH
WVPREKILTTNTWSSELSKLAANLFLAQRISSINSISALCEATGADVEEV
ATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQ
QVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSI
YISKYLMDEGAHLHIYDPKVPREQIVVDLSHPDQVSRLVTISKDPYEACD
GAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIG
FQIETIGKK
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 F 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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PDB6c58 The A225L Substitution of hUGDH alters structure and function
Resolution2.198 Å
Binding residue
(original residue number in PDB)		G13 Y14 V15 D36 V37 R41 V89 N90 T91 Y108 S130 T131 R346
Binding residue
(residue number reindexed from 1)		G12 Y13 V14 D35 V36 R40 V88 N89 T90 Y107 S129 T130 R345
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T131 E165 K220 N224 C276 D280
Catalytic site (residue number reindexed from 1) T130 E164 K219 N223 C275 D279
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
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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