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BioLiP

Structure of PDB 2q3e Chain D Binding Site BS01

Receptor Information

>2q3e Chain D (length=458) 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
YISKYLMDEGAHLHIYDPKVPREQIVVDLSDQVSRLVTISKDPYEACDGA
HAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQ
IETIGKKV

Ligand information

Ligand ID

NAI

InChI

InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

InChIKey

BOPGDPNILDQYTO-NNYOXOHSSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O

Formula

C21 H29 N7 O14 P2

Name

1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH

PDB chain

2q3e Chain D Residue 500 [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)	I10 G11 G13 Y14 V15 D36 V37 R41 V89 N90 T91 Y108 S130 T131 E161 L163 E165 C276 K279 R346
Binding residue (residue number reindexed from 1)	I9 G10 G12 Y13 V14 D35 V36 R40 V88 N89 T90 Y107 S129 T130 E160 L162 E164 C275 K278 R345
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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