Structure of PDB 6mk0 Chain A Binding Site BS06

Receptor Information
>6mk0 Chain A (length=920) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGI
VEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRS
KQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDAD
GQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVY
SIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTL
GMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDL
DQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSM
PPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVY
PSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLD
KLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRD
KLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQ
ADFIGVVRNNEALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFS
VHQQSEMDTSVKFDLQIQSSNLFDKVSPVVSHKVDLAVLAAVEIRGVSSP
DHVFLPIPNWEHKENPETEEDVGPVVQHIYELRNNGPSSFSKAMLHLQWP
YKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKIHTLGCGVAQCLKIVC
QVGRLDRGKSAILYVKSLLWTETFMNKENQNHSYSLKSSASFNVIEFPYK
NLPIEDITNSTLVTTNVTWG
Ligand information
Ligand IDJUY
InChIInChI=1S/C25H25N5O4S/c31-21(10-4-1-7-17-12-11-16-6-5-14-27-22(16)28-17)26-15-13-19(25(33)34)29-23(32)24-30-18-8-2-3-9-20(18)35-24/h2-3,5-6,8-9,11-12,14,19H,1,4,7,10,13,15H2,(H,26,31)(H,29,32)(H,33,34)/t19-/m0/s1
InChIKeyWHGYZWMTBKTNLT-IBGZPJMESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)nc(s2)C(=O)NC(CCNC(=O)CCCCc3ccc4cccnc4n3)C(=O)O
CACTVS 3.385OC(=O)[C@H](CCNC(=O)CCCCc1ccc2cccnc2n1)NC(=O)c3sc4ccccc4n3
ACDLabs 12.01C(C(NCCC(C(=O)O)NC(c2sc1c(cccc1)n2)=O)=O)CCCc3ccc4c(n3)nccc4
OpenEye OEToolkits 2.0.6c1ccc2c(c1)nc(s2)C(=O)N[C@@H](CCNC(=O)CCCCc3ccc4cccnc4n3)C(=O)O
CACTVS 3.385OC(=O)[CH](CCNC(=O)CCCCc1ccc2cccnc2n1)NC(=O)c3sc4ccccc4n3
FormulaC25 H25 N5 O4 S
Name(2S)-2-[(1,3-benzothiazole-2-carbonyl)amino]-4-{[5-(1,8-naphthyridin-2-yl)pentanoyl]amino}butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6mk0 Chain B Residue 712 [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)		Y178 D218
Binding residue
(residue number reindexed from 1)		Y178 D218
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0001846 opsonin binding
GO:0001968 fibronectin binding
GO:0002020 protease binding
GO:0005080 protein kinase C binding
GO:0005102 signaling receptor binding
GO:0005178 integrin binding
GO:0005245 voltage-gated calcium channel activity
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0017134 fibroblast growth factor binding
GO:0019960 C-X3-C chemokine binding
GO:0031994 insulin-like growth factor I binding
GO:0038132 neuregulin binding
GO:0046872 metal ion binding
GO:0050431 transforming growth factor beta binding
GO:0050840 extracellular matrix binding
GO:1990430 extracellular matrix protein binding
Biological Process
GO:0001525 angiogenesis
GO:0001568 blood vessel development
GO:0001570 vasculogenesis
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007229 integrin-mediated signaling pathway
GO:0008284 positive regulation of cell population proliferation
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0010888 negative regulation of lipid storage
GO:0016477 cell migration
GO:0030335 positive regulation of cell migration
GO:0031589 cell-substrate adhesion
GO:0032369 negative regulation of lipid transport
GO:0033627 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:0035313 wound healing, spreading of epidermal cells
GO:0035987 endodermal cell differentiation
GO:0038027 apolipoprotein A-I-mediated signaling pathway
GO:0043277 apoptotic cell clearance
GO:0045785 positive regulation of cell adhesion
GO:0046718 symbiont entry into host cell
GO:0050748 negative regulation of lipoprotein metabolic process
GO:0050764 regulation of phagocytosis
GO:0050919 negative chemotaxis
GO:0051057 positive regulation of small GTPase mediated signal transduction
GO:0070371 ERK1 and ERK2 cascade
GO:0070588 calcium ion transmembrane transport
GO:0071604 transforming growth factor beta production
GO:0085017 entry into host cell by a symbiont-containing vacuole
GO:0097192 extrinsic apoptotic signaling pathway in absence of ligand
GO:0098609 cell-cell adhesion
GO:1902533 positive regulation of intracellular signal transduction
GO:1905598 negative regulation of low-density lipoprotein receptor activity
GO:2000536 negative regulation of entry of bacterium into host cell
GO:2001237 negative regulation of extrinsic apoptotic signaling pathway
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0008305 integrin complex
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0031258 lamellipodium membrane
GO:0031527 filopodium membrane
GO:0031528 microvillus membrane
GO:0032587 ruffle membrane
GO:0034682 integrin alphav-beta1 complex
GO:0034683 integrin alphav-beta3 complex
GO:0034684 integrin alphav-beta5 complex
GO:0034685 integrin alphav-beta6 complex
GO:0034686 integrin alphav-beta8 complex
GO:0035579 specific granule membrane
GO:0035866 alphav-beta3 integrin-PKCalpha complex
GO:0035867 alphav-beta3 integrin-IGF-1-IGF1R complex
GO:0035868 alphav-beta3 integrin-HMGB1 complex
GO:0045335 phagocytic vesicle
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:6mk0, PDBe:6mk0, PDBj:6mk0
PDBsum6mk0
PubMed
UniProtP06756|ITAV_HUMAN Integrin alpha-V (Gene Name=ITGAV)

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