Structure of PDB 8u4p Chain R Binding Site BS01

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 IDCLR
InChIInChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyHVYWMOMLDIMFJA-DPAQBDIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
CACTVS 3.341CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
OpenEye OEToolkits 1.5.0CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
CACTVS 3.341CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
FormulaC27 H46 O
NameCHOLESTEROL
ChEMBLCHEMBL112570
DrugBankDB04540
ZINCZINC000003875383
PDB chain8u4p Chain R Residue 701 [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)		L78 H79 Y157
Binding residue
(residue number reindexed from 1)		L46 H47 Y125
Annotation score4
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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