compound 1 [Vakkeel et al., 2018]   Click here for help

GtoPdb Ligand ID: 9895

Compound class: Synthetic organic
Comment: Compound 1 is a photoactivatable α5β1 integrin ligand [4]. Structurally it is a selective α5β1 integrin ligand (a peptidomimetic of the RGD adhesive motif found in several extracellular matrix (ECM) proteins) linked to a 3-(4,5-Dimethoxy-2-nitrophenyl)-2-butyl ester (DMNPB) photocleavable chromophore. When intact, the compound is unable to bind the integrin, but upon exposure to light the chromophore is cleaved and the ligand then behaves as an antagonist of α5β1 interaction with ECM substrates. The photactivation of compound 1 allows precise, in situ, dose-responsive and temporal study of the role played by α5β1 integrin-dependent processes in cell adhesion and migration.
α5β1 integrin is a molecular target that plays recognised roles in tumour angiogenesis and cancer cell migration and metastasis [3,5], that is being expoilted for clinical utility in cancer indications [2,6,8]. α5β1 may also be an immune system/inflammation relevant target [1,7].
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 13
Hydrogen bond donors 6
Rotatable bonds 25
Topological polar surface area 258.69
Molecular weight 790.34
XLogP 4.33
No. Lipinski's rules broken 3
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES [N-]=[N+]=NCCCOc1cc(C)c(c(c1)C)C(=O)NC(C(=O)OC(C(c1cc(OC)c(cc1[N+](=O)[O-])OC)C)C)CNC(=O)CNC(=O)c1cccc(c1)NC(=N)N
Isomeric SMILES [N-]=[N+]=NCCCOc1cc(C)c(c(c1)C)C(=O)NC(C(=O)OC(C(c1cc(OC)c(cc1[N+](=O)[O-])OC)C)C)CNC(=O)CNC(=O)c1cccc(c1)NC(=N)N
InChI InChI=1S/C37H46N10O10/c1-20-13-26(56-12-8-11-43-46-40)14-21(2)33(20)35(50)45-28(18-41-32(48)19-42-34(49)24-9-7-10-25(15-24)44-37(38)39)36(51)57-23(4)22(3)27-16-30(54-5)31(55-6)17-29(27)47(52)53/h7,9-10,13-17,22-23,28H,8,11-12,18-19H2,1-6H3,(H,41,48)(H,42,49)(H,45,50)(H4,38,39,44)
InChI Key CCIKYPZLPYEMFX-UHFFFAOYSA-N
Bioactivity Comments
Intact compound 1 does not bind to the integrin target, thefore we cannot map a primary protein target for this entity. However, direct interaction of cellular α5β1 with cleaved (activated) compound 1 was determined in assays in which HUVEC cells were shown to bind to immobilised compound 1 ONLY when the ligand was photoactivated [4].