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BioLiP

Structure of PDB 2q3e Chain E Binding Site BS02

Receptor Information

>2q3e Chain E (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
WVPREKILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEV
ATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQ
QVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSI
YISKYLMDEGAHLHIYDPKVPREQIVVDLSHDQVSRLVTISKDPYEACDG
AHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGF
QIETIGKKV

Ligand information

Ligand ID

UPG

InChI

InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1

InChIKey

HSCJRCZFDFQWRP-JZMIEXBBSA-N

SMILES

Software	SMILES
CACTVS 3.370	OC[C@H]1O[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](O)[C@@H]1O
ACDLabs 12.01	O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
CACTVS 3.370	OC[CH]1O[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](O)[CH]1O
OpenEye OEToolkits 1.7.6	C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
OpenEye OEToolkits 1.7.6	C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O

Formula

C15 H24 N2 O17 P2

Name

URIDINE-5'-DIPHOSPHATE-GLUCOSE;
URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER

PDB chain

2q3e Chain E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2q3e Structure and mechanism of human UDP-glucose 6-dehydrogenase.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	F162 L163 A164 E165 K220 I231 F265 K267 S269 F272 G273 C276 F277 F338 K339 R442
Binding residue (residue number reindexed from 1)	F161 L162 A163 E164 K219 I230 F264 K266 S268 F271 G272 C275 F276 F337 K338 R435
Annotation score	4

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

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Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:2q3e, PDBe:2q3e, PDBj:2q3e
PDBsum	2q3e
PubMed	21502315
UniProt	O60701\|UGDH_HUMAN UDP-glucose 6-dehydrogenase (Gene Name=UGDH)

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