Structure of PDB 7d73 Chain C Binding Site BS01

Receptor Information
>7d73 Chain C (length=406) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKAVILIGGPQKGTRFRPLSFEVPKPLFPVAGVPMIQHHIEACAQVPGM
QEILLIGFYQPDEPLTQFLEAAQQEFNLPVRYLQEFAPLGTGGGLYHFRD
QILAGSPEAFFVLNADVCSDFPLSAMLEAHRRQRHPFLLLGTTANRTQSL
NYGCIVENPQTHEVLHYVEKPSTFISDIINCGIYLFSPEALKPLRDVFQR
NQQGTIRLEQDVFSALAGQGQIYVHLTDGIWSQIKSAGSALYASRLYLSR
YQDTHPERLAKHTPGGPWIRGNVYIHPTAKVAPSAVLGPNVSIGKGVTVG
EGVRLRESIVLHGATLQEHTCVLHSIVGWGSTVGRWARVEGTPSDPNPND
PRARMDSESLFKDGKLLPAITILGCRVRIPAEVLILNSIVLPHKELSRSF
TNQIIL
Ligand information
Ligand IDGDD
InChIInChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyMVMSCBBUIHUTGJ-GDJBGNAASA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC16 H25 N5 O16 P2
NameGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
ChEMBL
DrugBank
ZINCZINC000008215581
PDB chain7d73 Chain C Residue 501 [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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PDB7d73 Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		L7 I8 G9 K13 I56 E85 G90 T91 N114 A115 D116 Y152 E169 N180 E223 W245 Q247 K249
Binding residue
(residue number reindexed from 1)		L7 I8 G9 K13 I56 E85 G90 T91 N114 A115 D116 Y152 E169 N180 E209 W231 Q233 K235
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity
GO:0004857 enzyme inhibitor activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0019899 enzyme binding
Biological Process
GO:0006486 protein glycosylation
GO:0009058 biosynthetic process
GO:0009100 glycoprotein metabolic process
GO:0009298 GDP-mannose biosynthetic process
GO:0009890 negative regulation of biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0021537 telencephalon development
GO:0045934 negative regulation of nucleobase-containing compound metabolic process
GO:0045936 negative regulation of phosphate metabolic process
GO:0048644 muscle organ morphogenesis
GO:0050890 cognition
GO:0050905 neuromuscular process
GO:0051402 neuron apoptotic process
GO:0060538 skeletal muscle organ development
GO:0061744 motor behavior
GO:0062014 negative regulation of small molecule metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome
GO:0120508 GDP-mannose pyrophosphorylase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7d73, PDBe:7d73, PDBj:7d73
PDBsum7d73
PubMed33986552
UniProtQ96IJ6|GMPPA_HUMAN Mannose-1-phosphate guanyltransferase alpha (Gene Name=GMPPA)

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