Structure of PDB 5tc3 Chain A Binding Site BS03

Receptor Information
>5tc3 Chain A (length=488) Species: 284811 (Eremothecium gossypii ATCC 10895) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYRDAATALEHLATYAEKDGLSVEQLMDSKTGGLTYNDFLVLPGKIDFPS
SEVVLSSRLTKKITLNAPFVSSPMDTVTEADMAIHMALLGGIGIIHHNCT
AEEQAEMVRRVKKYENGFINAPVVVGPDATVADVRRMKNEFGFAGFPVTD
DGKPTGKLQGIITSRDIQFVEDETLLVSEIMTKDVITGKQGINLEEANQI
LKNTKKGKLPIVDEAGCLVSMLSRTDLMKNQSYPLASKSADTKQLLCGAA
IGTIDADRQRLAMLVEAGLDVVVLDSSQGNSVFQINMIKWIKETFPDLQV
IAGNVVTREQAASLIHAGADGLRIGMGSGSICITQEVMACGRPQGTAVYN
VTQFANQFGVPCIADGGVQNIGHITKAIALGASTVMMGGMLAGTTESPGE
YFRRLKTYRGSIDAAQGVTGSVIDKGSIKKYIPYLYNGLQHSCQDIGVRS
LVEFREKVDSGSVRFEFRTPSAQLEGGVHNLHSYELFD
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 chain5tc3 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5tc3 A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.
Resolution2.462 Å
Binding residue
(original residue number in PDB)		K115 N118 I121 P124 V125 F145 A146 G147 K210 M223 S225 T227 D228 K231
Binding residue
(residue number reindexed from 1)		K113 N116 I119 P122 V123 F143 A144 G145 K208 M221 S223 T225 D226 K229
Annotation score2
Enzymatic activity
Enzyme Commision number 1.1.1.205: IMP dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0003938 IMP dehydrogenase activity
GO:0005524 ATP 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
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5tc3, PDBe:5tc3, PDBj:5tc3
PDBsum5tc3
PubMed28572600
UniProtQ756Z6

[Back to BioLiP]