Structure of PDB 6udq Chain D Binding Site BS03

Receptor Information
>6udq Chain D (length=487) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITL
KTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYE
QGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSR
DIDFLKEEEHDCFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPI
VNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLD
LLAQAGVDVVVLDSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAK
NLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPV
IADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKY
RGMGSLDAMIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLT
QVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain6udq Chain D Residue 602 [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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PDB6udq Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.
Resolution3.27 Å
Binding residue
(original residue number in PDB)		P118 F139 C140 G141 S160 K208 T225 D226
Binding residue
(residue number reindexed from 1)		P107 F128 C129 G130 S149 K197 T214 D215
Annotation score2
Enzymatic activity
Enzyme Commision number 1.1.1.205: IMP dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003824 catalytic activity
GO:0003938 IMP dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006177 GMP biosynthetic process
GO:0006183 GTP biosynthetic process
GO:0007623 circadian rhythm
GO:0046651 lymphocyte proliferation
GO:0071353 cellular response to interleukin-4
GO:0097294 'de novo' XMP biosynthetic process
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005778 peroxisomal membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6udq, PDBe:6udq, PDBj:6udq
PDBsum6udq
PubMed31999252
UniProtP12268|IMDH2_HUMAN Inosine-5'-monophosphate dehydrogenase 2 (Gene Name=IMPDH2)

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