Structure of PDB 5vr8 Chain C Binding Site BS01

Receptor Information
>5vr8 Chain C (length=462) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPT
LPIYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMG
KGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTK
PNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVY
EHWVPREKILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVE
EVATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARY
WQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESS
SIYISKYLMDEGAHLHIYDPKVPREQIVVDLSHEDDQVSRLVTISKDPYE
ACDGAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQ
TIGFQIETIGKK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5vr8 Chain C Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vr8 The entropic force generated by intrinsically disordered segments tunes protein function.
Resolution1.999 Å
Binding residue
(original residue number in PDB)		I10 G13 Y14 D36 V37 R41 V89 N90 C112 R346
Binding residue
(residue number reindexed from 1)		I11 G14 Y15 D37 V38 R42 V90 N91 C113 R347
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T131 E165 K220 N224 C276 D280
Catalytic site (residue number reindexed from 1) T132 E166 K221 N225 C277 D281
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
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Cellular Component
External links
PDB RCSB:5vr8, PDBe:5vr8, PDBj:5vr8
PDBsum5vr8
PubMed30420606
UniProtO60701|UGDH_HUMAN UDP-glucose 6-dehydrogenase (Gene Name=UGDH)

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