Structure of PDB 2vmd Chain A Binding Site BS02

Receptor Information
>2vmd Chain A (length=252) Species: 366501 (Dictyostelium discoideum AX2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSVSCLANALLNLRSSTDYNADHGVKNSILNFSNSKDASRFDGSESWSSS
VLDKNQFIVAGSDSVKHFVAISTQGRGDHDQWVTSYKLRYTLDNVNWVEY
NNGEIINANKDRNSIVTINFNPPIKARSIAIHPQTYNNHISLRWELYALP
VKSYSNPSVQVGEVSIGDRSLNSGTGSRTIVRHVKFPVEFLSVPIVSIGC
KKVDAHTDNGQMRWEGKSENITTKGFDLTFITWGNNAVYDLTFDYVAVEF
NN
Ligand information
Ligand IDMBG
InChIInChI=1S/C7H14O6/c1-12-7-6(11)5(10)4(9)3(2-8)13-7/h3-11H,2H2,1H3/t3-,4+,5+,6-,7-/m1/s1
InChIKeyHOVAGTYPODGVJG-VOQCIKJUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04OC1C(O)C(O)C(OC1OC)CO
OpenEye OEToolkits 1.5.0CO[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O
CACTVS 3.341CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.341CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.5.0COC1C(C(C(C(O1)CO)O)O)O
FormulaC7 H14 O6
Namemethyl beta-D-galactopyranoside;
METHYL-BETA-GALACTOSE;
methyl beta-D-galactoside;
methyl D-galactoside;
methyl galactoside
ChEMBLCHEMBL442951
DrugBankDB04046
ZINCZINC000004096161
PDB chain2vmd Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vmd Structure Determination of Discoidin II from Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q216 R218 W238
Binding residue
(residue number reindexed from 1)		Q211 R213 W233
Annotation score1
Binding affinityMOAD: Kd=0.95mM
PDBbind-CN: -logKd/Ki=3.02,Kd=0.95mM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016936 galactoside binding
GO:0030246 carbohydrate binding
GO:0030247 polysaccharide binding
GO:0046871 N-acetylgalactosamine binding
GO:0046872 metal ion binding
GO:0070492 oligosaccharide binding
Biological Process
GO:0007010 cytoskeleton organization
GO:0007155 cell adhesion
GO:0009617 response to bacterium
GO:0098609 cell-cell adhesion
GO:0140582 adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009986 cell surface
GO:0031012 extracellular matrix
GO:0031160 spore wall
GO:0031982 vesicle
GO:0045335 phagocytic vesicle
GO:0098636 protein complex involved in cell adhesion

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2vmd, PDBe:2vmd, PDBj:2vmd
PDBsum2vmd
PubMed18384150
UniProtP42530|DIS2_DICDI Discoidin-2 (Gene Name=dscE)

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