Structure of PDB 6mk0 Chain B Binding Site BS02

Receptor Information
>6mk0 Chain B (length=687) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPES
IEFPVSEARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQ
VRQVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGF
GAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRF
NEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAK
THIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKN
INLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRS
KVELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKV
RGCPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNG
TFECGVCRCGPGWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLC
GQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDW
TGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEKCPT
CPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAV
NCTYKNEDDCVVRFQYYEDSSGKSILYVVEEPECPKG
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain6mk0 Chain B Residue 709 [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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PDB6mk0 Novel Pure alphaVbeta3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations
Resolution3.005 Å
Binding residue
(original residue number in PDB)		S123 D126 D127 M335
Binding residue
(residue number reindexed from 1)		S120 D123 D124 M332
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0001968 fibronectin binding
GO:0002020 protease binding
GO:0003756 protein disulfide isomerase activity
GO:0005080 protein kinase C binding
GO:0005161 platelet-derived growth factor receptor binding
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0017134 fibroblast growth factor binding
GO:0019899 enzyme binding
GO:0019960 C-X3-C chemokine binding
GO:0031994 insulin-like growth factor I binding
GO:0038132 neuregulin binding
GO:0042802 identical protein binding
GO:0043184 vascular endothelial growth factor receptor 2 binding
GO:0046872 metal ion binding
GO:0050839 cell adhesion molecule binding
GO:0050840 extracellular matrix binding
GO:0070051 fibrinogen binding
Biological Process
GO:0001934 positive regulation of protein phosphorylation
GO:0001938 positive regulation of endothelial cell proliferation
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002687 positive regulation of leukocyte migration
GO:0007044 cell-substrate junction assembly
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0007566 embryo implantation
GO:0007596 blood coagulation
GO:0008277 regulation of G protein-coupled receptor signaling pathway
GO:0010595 positive regulation of endothelial cell migration
GO:0010628 positive regulation of gene expression
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0010763 positive regulation of fibroblast migration
GO:0010888 negative regulation of lipid storage
GO:0014823 response to activity
GO:0014909 smooth muscle cell migration
GO:0014911 positive regulation of smooth muscle cell migration
GO:0030168 platelet activation
GO:0030335 positive regulation of cell migration
GO:0030949 positive regulation of vascular endothelial growth factor receptor signaling pathway
GO:0031589 cell-substrate adhesion
GO:0032147 activation of protein kinase activity
GO:0032369 negative regulation of lipid transport
GO:0032880 regulation of protein localization
GO:0032956 regulation of actin cytoskeleton organization
GO:0033627 cell adhesion mediated by integrin
GO:0033630 positive regulation of cell adhesion mediated by integrin
GO:0033690 positive regulation of osteoblast proliferation
GO:0034113 heterotypic cell-cell adhesion
GO:0034446 substrate adhesion-dependent cell spreading
GO:0035295 tube development
GO:0035313 wound healing, spreading of epidermal cells
GO:0036119 response to platelet-derived growth factor
GO:0036120 cellular response to platelet-derived growth factor stimulus
GO:0038027 apolipoprotein A-I-mediated signaling pathway
GO:0042060 wound healing
GO:0043277 apoptotic cell clearance
GO:0045124 regulation of bone resorption
GO:0045766 positive regulation of angiogenesis
GO:0045780 positive regulation of bone resorption
GO:0046718 symbiont entry into host cell
GO:0048008 platelet-derived growth factor receptor signaling pathway
GO:0048146 positive regulation of fibroblast proliferation
GO:0048333 mesodermal cell differentiation
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0050748 negative regulation of lipoprotein metabolic process
GO:0050919 negative chemotaxis
GO:0051279 regulation of release of sequestered calcium ion into cytosol
GO:0051611 regulation of serotonin uptake
GO:0060055 angiogenesis involved in wound healing
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0070527 platelet aggregation
GO:0071260 cellular response to mechanical stimulus
GO:0071466 cellular response to xenobiotic stimulus
GO:0072126 positive regulation of glomerular mesangial cell proliferation
GO:0072378 blood coagulation, fibrin clot formation
GO:0098880 maintenance of postsynaptic specialization structure
GO:0099149 regulation of postsynaptic neurotransmitter receptor internalization
GO:0150054 regulation of postsynaptic neurotransmitter receptor diffusion trapping
GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
GO:1900731 positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway
GO:1901163 regulation of trophoblast cell migration
GO:1903053 regulation of extracellular matrix organization
GO:1905598 negative regulation of low-density lipoprotein receptor activity
GO:1990314 cellular response to insulin-like growth factor stimulus
GO:2000352 negative regulation of endothelial cell apoptotic process
GO:2000406 positive regulation of T cell migration
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0008305 integrin complex
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016324 apical plasma membrane
GO:0031092 platelet alpha granule membrane
GO:0031258 lamellipodium membrane
GO:0031527 filopodium membrane
GO:0031528 microvillus membrane
GO:0032587 ruffle membrane
GO:0032991 protein-containing complex
GO:0034683 integrin alphav-beta3 complex
GO:0035866 alphav-beta3 integrin-PKCalpha complex
GO:0035867 alphav-beta3 integrin-IGF-1-IGF1R complex
GO:0035868 alphav-beta3 integrin-HMGB1 complex
GO:0042470 melanosome
GO:0042995 cell projection
GO:0043235 receptor complex
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0070062 extracellular exosome
GO:0070161 anchoring junction
GO:0070442 integrin alphaIIb-beta3 complex
GO:0071062 alphav-beta3 integrin-vitronectin complex
GO:0071133 alpha9-beta1 integrin-ADAM8 complex
GO:0097060 synaptic membrane
GO:0098690 glycinergic synapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6mk0, PDBe:6mk0, PDBj:6mk0
PDBsum6mk0
PubMed
UniProtP05106|ITB3_HUMAN Integrin beta-3 (Gene Name=ITGB3)

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