Structure of PDB 3gpd Chain R Binding Site BS01

Receptor Information
>3gpd Chain R (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKVKVGVDGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLHYMVYMFQYDS
THGKFHGTVKAEDGKLVIDGKAITIFQERDPENIKWGDAGTAYVVESTGV
FTTMEKAGAHLKGGAKRIVISAPSADAPMFVMGVNHFKYANSLKIISNAS
CTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDSPSGKLWRGGRG
AAQNLIPASTGAAKAVGKVIPELDGKLTGMAFRVPTANVSVLDLTCRLEK
PAKYDDIKKVVKEASEGPLKGILGYTEDEVVSDDFNGSNHSSIFDAGAGI
ELNDTFVKLVSWYDNEFGYSERVVDLMAHMASKE
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain3gpd Chain R Residue 336 [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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PDB3gpd Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		G9 G11 R12 I13 N33 P35 F36 E78 S97 T98 S121 A122 C151 E316
Binding residue
(residue number reindexed from 1)		G9 G11 R12 I13 N33 P35 F36 E78 S97 T98 S121 A122 C151 E316
Annotation score4
Enzymatic activity
Enzyme Commision number 1.2.1.12: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).
2.6.99.-
Gene Ontology
Molecular Function
GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0016740 transferase activity
GO:0019828 aspartic-type endopeptidase inhibitor activity
GO:0035605 peptidyl-cysteine S-nitrosylase activity
GO:0042802 identical protein binding
GO:0050661 NADP binding
GO:0051287 NAD binding
GO:0097718 disordered domain specific binding
Biological Process
GO:0000226 microtubule cytoskeleton organization
GO:0001819 positive regulation of cytokine production
GO:0006006 glucose metabolic process
GO:0006096 glycolytic process
GO:0006417 regulation of translation
GO:0006915 apoptotic process
GO:0010951 negative regulation of endopeptidase activity
GO:0016241 regulation of macroautophagy
GO:0017148 negative regulation of translation
GO:0031640 killing of cells of another organism
GO:0032481 positive regulation of type I interferon production
GO:0035606 peptidyl-cysteine S-trans-nitrosylation
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0045087 innate immune response
GO:0050821 protein stabilization
GO:0050832 defense response to fungus
GO:0051402 neuron apoptotic process
GO:0051873 killing by host of symbiont cells
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0071346 cellular response to type II interferon
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0015630 microtubule cytoskeleton
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0031982 vesicle
GO:0043231 intracellular membrane-bounded organelle
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0097452 GAIT complex
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3gpd, PDBe:3gpd, PDBj:3gpd
PDBsum3gpd
PubMed957435
UniProtP04406|G3P_HUMAN Glyceraldehyde-3-phosphate dehydrogenase (Gene Name=GAPDH)

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