Structure of PDB 6i0m Chain A Binding Site BS03

Receptor Information
>6i0m Chain A (length=450) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITL
KTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYE
QGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSR
DIDFLEHDCFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPIVNE
DDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLA
QAGVDVVVLDSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAKNLI
DAGVDALRVGMGSGSITQEVLACGRPQATAVYKVSEYARRFGVPVIADGG
IQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGMGSLDAQDKGS
IHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGG
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain6i0m Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6i0m A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity.
Resolution2.567 Å
Binding residue
(original residue number in PDB)		F139 C140 G141 K208 T225 D226
Binding residue
(residue number reindexed from 1)		F128 C129 G130 K194 T211 D212
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6i0m, PDBe:6i0m, PDBj:6i0m
PDBsum6i0m
PubMed30664871
UniProtP12268|IMDH2_HUMAN Inosine-5'-monophosphate dehydrogenase 2 (Gene Name=IMPDH2)

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