Structure of PDB 5ogk Chain A Binding Site BS01

Receptor Information
>5ogk Chain A (length=292) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSGPISILSYCGSSILMTVTNKFVVNLKDFNMNFVMLFVQSLVCTITLII
LRILGFRSLNKTDAKNWFPISFLLVLMIYTSSKALQYLAVPIYTIFKNLT
IILIAYGEVLFFGGSVTSMELSSFLLMVLSSVVATWGDQQNPGYFWMFTN
CITSALFVLIMRKRIKLTNFKDFDTMFYNNVLALPILLLFSFCVEDWSSV
NLTNNFSNDSLTAMIISGVASVGISYCSGWCVRVTSSTTYSMVGALNKLP
IALSGLIFFDAPRNFLSILSIFIGFLSGIIYAVAKQKKQQAQ
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 chain5ogk Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ogk Structural basis of nucleotide sugar transport across the Golgi membrane.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		Y28 M35 Y114 I265 S266 S269 Y281 K289
Binding residue
(residue number reindexed from 1)		Y10 M17 Y93 I224 S225 S228 Y240 K248
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=5.11,IC50=7.7uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005458 GDP-mannose transmembrane transporter activity
GO:0015297 antiporter activity
Biological Process
GO:0055085 transmembrane transport
GO:1990570 GDP-mannose transmembrane transport
Cellular Component
GO:0000139 Golgi membrane
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ogk, PDBe:5ogk, PDBj:5ogk
PDBsum5ogk
PubMed29143814
UniProtP40107|GMT1_YEAST GDP-mannose transporter 1 (Gene Name=VRG4)

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