Structure of PDB 2nwg Chain B Binding Site BS01

Receptor Information
>2nwg Chain B (length=64) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSYRCPCRFFESHIARANVKHLKILNTPNCALQIVARLKNNNRQVCIDP
KLKWIQEYLEKALN
Ligand information
Ligand IDSGN
InChIInChI=1S/C6H13NO11S2/c8-4-2(1-17-20(14,15)16)18-6(10)3(5(4)9)7-19(11,12)13/h2-10H,1H2,(H,11,12,13)(H,14,15,16)/t2-,3-,4-,5-,6+/m1/s1
InChIKeyDQTRACMFIGDHSN-UKFBFLRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O
CACTVS 3.341O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O)[CH]1N[S](O)(=O)=O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O
ACDLabs 10.04O=S(=O)(O)OCC1OC(O)C(NS(=O)(=O)O)C(O)C1O
CACTVS 3.341O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1N[S](O)(=O)=O
FormulaC6 H13 N O11 S2
Name2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose;
N,O6-DISULFO-GLUCOSAMINE;
6-O-sulfo-N-sulfo-alpha-D-glucosamine;
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose;
2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose;
2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose
ChEMBL
DrugBankDB03959
ZINC
PDB chain2nwg Chain C Residue 1 [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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PDB2nwg Structural and Functional Basis of CXCL12 (Stromal Cell-derived Factor-1{alpha}) Binding to Heparin
Resolution2.07 Å
Binding residue
(original residue number in PDB)		H25 R41
Binding residue
(residue number reindexed from 1)		H22 R38
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005102 signaling receptor binding
GO:0005125 cytokine activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008009 chemokine activity
GO:0008083 growth factor activity
GO:0042379 chemokine receptor binding
GO:0045236 CXCR chemokine receptor binding
Biological Process
GO:0001666 response to hypoxia
GO:0001764 neuron migration
GO:0001938 positive regulation of endothelial cell proliferation
GO:0006874 intracellular calcium ion homeostasis
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007411 axon guidance
GO:0008015 blood circulation
GO:0008064 regulation of actin polymerization or depolymerization
GO:0008284 positive regulation of cell population proliferation
GO:0008344 adult locomotory behavior
GO:0009612 response to mechanical stimulus
GO:0009615 response to virus
GO:0022029 telencephalon cell migration
GO:0030335 positive regulation of cell migration
GO:0031100 animal organ regeneration
GO:0033603 positive regulation of dopamine secretion
GO:0033622 integrin activation
GO:0038146 chemokine (C-X-C motif) ligand 12 signaling pathway
GO:0038160 CXCL12-activated CXCR4 signaling pathway
GO:0043434 response to peptide hormone
GO:0045666 positive regulation of neuron differentiation
GO:0045785 positive regulation of cell adhesion
GO:0048842 positive regulation of axon extension involved in axon guidance
GO:0050930 induction of positive chemotaxis
GO:0050965 detection of temperature stimulus involved in sensory perception of pain
GO:0050966 detection of mechanical stimulus involved in sensory perception of pain
GO:0051924 regulation of calcium ion transport
GO:0060326 cell chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0090026 positive regulation of monocyte chemotaxis
GO:0090280 positive regulation of calcium ion import
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1903237 negative regulation of leukocyte tethering or rolling
GO:1904018 positive regulation of vasculature development
GO:1990478 response to ultrasound
GO:1990869 cellular response to chemokine
GO:2000406 positive regulation of T cell migration
GO:2000669 negative regulation of dendritic cell apoptotic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0009897 external side of plasma membrane
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2nwg, PDBe:2nwg, PDBj:2nwg
PDBsum2nwg
PubMed17264079
UniProtP48061|SDF1_HUMAN Stromal cell-derived factor 1 (Gene Name=CXCL12)

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