Structure of PDB 7d72 Chain J Binding Site BS01

Receptor Information
>7d72 Chain J (length=360) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKALILVGGYGTRLRPLTLSTPKPLVDFCNKPILLHQVEALAAAGVDHVI
LAVSYMSQVLEKEMKAQEQRLGIRISMSHEEEPLGTAGPLALARDLLSET
ADPFFVLNSDVICDFPFQAMVQFHRHHGQEGSILVTKVEEPSKYGVVVCE
ADTGRIHRFVEKPQVFVSNKINAGMYILSPAVLQRIQLQPTSIEKEVFPI
MAKEGQLYAMELQGFWMDIGQPKDFLTGMCLFLQSLRQKQPERLCSGPGI
VGNVLVDPSARIGQNCSIGPNVSLGPGVVVEDGVCIRRCTVLRDARIRSH
SWLESCIVGWRCRVGQWVRMENVTVLGEDVIVNDELYLNGASVLPHKSIG
ESVPEPRIIM
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 chain7d72 Chain J 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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PDB7d72 Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		L6 V7 G85 N108 S109 D110 G145 N172 W216
Binding residue
(residue number reindexed from 1)		L6 V7 G85 N108 S109 D110 G145 N172 W216
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.13: mannose-1-phosphate guanylyltransferase.
Gene Ontology
Molecular Function
GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0009058 biosynthetic process
GO:0009298 GDP-mannose biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0061728 GDP-mannose biosynthetic process from mannose
GO:0141199 GDP-mannose biosynthetic process from glucose
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
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:7d72, PDBe:7d72, PDBj:7d72
PDBsum7d72
PubMed33986552
UniProtQ9Y5P6|GMPPB_HUMAN Mannose-1-phosphate guanyltransferase beta (Gene Name=GMPPB)

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