Structure of PDB 8u4p Chain R Binding Site BS02

Receptor Information
>8u4p Chain R (length=286) Species: 6100,9606 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSV
ADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVSLYSSVLILAFISL
DRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADD
RYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGH
QKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHK
WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALT
Ligand information
Ligand IDVH6
InChIInChI=1S/C28H54N8/c1-9-29-15-17-31-13-3-21-35(23-19-33-11-1)25-27-5-7-28(8-6-27)26-36-22-4-14-32-18-16-30-10-2-12-34-20-24-36/h5-8,29-34H,1-4,9-26H2
InChIKeyYIQPUIGJQJDJOS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1NCCCNCCN(Cc2ccc(CN3CCCNCCNCCCNCC3)cc2)CCCNC1
OpenEye OEToolkits 2.0.7c1cc(ccc1CN2CCCNCCNCCCNCC2)CN3CCCNCCNCCCNCC3
CACTVS 3.385C1CNCCNCCCN(CCNC1)Cc2ccc(CN3CCCNCCNCCCNCC3)cc2
FormulaC28 H54 N8
NamePlerixafor;
1,1'-[1,4-phenylenebis(methylene)]bis(1,4,8,11-tetraazacyclotetradecane);
AMD3100
ChEMBL
DrugBank
ZINC
PDB chain8u4p Chain R Residue 702 [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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PDB8u4p Structural insights into CXCR4 modulation and oligomerization
Resolution3.15 Å
Binding residue
(original residue number in PDB)		Y116 D262 H281 I284 E288
Binding residue
(residue number reindexed from 1)		Y84 D230 H249 I252 E256
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0003674 molecular_function
GO:0003779 actin binding
GO:0004930 G protein-coupled receptor activity
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0016493 C-C chemokine receptor activity
GO:0016494 C-X-C chemokine receptor activity
GO:0019955 cytokine binding
GO:0019957 C-C chemokine binding
GO:0031625 ubiquitin protein ligase binding
GO:0032027 myosin light chain binding
GO:0036094 small molecule binding
GO:0038147 C-X-C motif chemokine 12 receptor activity
GO:0043130 ubiquitin binding
Biological Process
GO:0001666 response to hypoxia
GO:0001764 neuron migration
GO:0002064 epithelial cell development
GO:0002407 dendritic cell chemotaxis
GO:0006091 generation of precursor metabolites and energy
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007420 brain development
GO:0008038 neuron recognition
GO:0008218 bioluminescence
GO:0009615 response to virus
GO:0014070 response to organic cyclic compound
GO:0014823 response to activity
GO:0016477 cell migration
GO:0019722 calcium-mediated signaling
GO:0022008 neurogenesis
GO:0022029 telencephalon cell migration
GO:0030155 regulation of cell adhesion
GO:0030335 positive regulation of cell migration
GO:0035470 positive regulation of vascular wound healing
GO:0038160 CXCL12-activated CXCR4 signaling pathway
GO:0043067 regulation of programmed cell death
GO:0043217 myelin maintenance
GO:0045446 endothelial cell differentiation
GO:0046718 symbiont entry into host cell
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0050769 positive regulation of neurogenesis
GO:0050792 regulation of viral process
GO:0050920 regulation of chemotaxis
GO:0050921 positive regulation of 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:0060048 cardiac muscle contraction
GO:0060326 cell chemotaxis
GO:0061154 endothelial tube morphogenesis
GO:0070098 chemokine-mediated signaling pathway
GO:0071345 cellular response to cytokine stimulus
GO:0071466 cellular response to xenobiotic stimulus
GO:0120162 positive regulation of cold-induced thermogenesis
GO:1901327 response to tacrolimus
GO:1903861 positive regulation of dendrite extension
GO:1904018 positive regulation of vasculature development
GO:1905322 positive regulation of mesenchymal stem cell migration
GO:1990478 response to ultrasound
GO:2000448 positive regulation of macrophage migration inhibitory factor signaling pathway
Cellular Component
GO:0005575 cellular_component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0031252 cell leading edge
GO:0031410 cytoplasmic vesicle
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome
GO:0070161 anchoring junction

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8u4p, PDBe:8u4p, PDBj:8u4p
PDBsum8u4p
PubMed
UniProtP42212|GFP_AEQVI Green fluorescent protein (Gene Name=GFP);
P61073|CXCR4_HUMAN C-X-C chemokine receptor type 4 (Gene Name=CXCR4)

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