Structure of PDB 8grd Chain B Binding Site BS01

Receptor Information
>8grd Chain B (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FPVTMLPGDGVGPELMHAVKEVFKAAAVPVEFQEHHLSEVQMASEEKLEQ
VLSSMKENKVAIIGKIHLASYDMRLRRKLDLFANVVHVKSLPGYMTRHNN
LDLVIIREQTEGEYSSLEHESARGVIECLKIVTRAKSQRIAKFAFDYATK
KGRGKVTAVHKANIMKLGDGLFLQCCEEVAELYPKIKFETMIIDNCCMQL
VQNPYQFDVLVMPNLYGNIIDNLAAGLVGGAGVVPGESYSAEYAVFETGA
RHPFAQAVGRNIANPTAMLLSASNMLRHLNLEYHSSMIADAVKKVIKVGK
VRTSDMGGYATCHDFTEEICRRVKDLD
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 chain8grd Chain B Residue 401 [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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PDB8grd Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.
Resolution2.699 Å
Binding residue
(original residue number in PDB)		A254 G255 H275 F277 N287
Binding residue
(residue number reindexed from 1)		A231 G232 H252 F254 N264
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0006099 tricarboxylic acid cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8grd, PDBe:8grd, PDBj:8grd
PDBsum8grd
PubMed36375638
UniProtO43837|IDH3B_HUMAN Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (Gene Name=IDH3B)

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