rivipansel   Click here for help

GtoPdb Ligand ID: 8307

Synonyms: GMI-1070 | PF-06460031 | PF-0646003102
Compound class: Synthetic organic
Comment: Rivipansel is a synthetic glycomimetic molecule, rationally designed as a pan-selectin inhibitor [1].
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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.

✖
Hydrogen bond acceptors 35
Hydrogen bond donors 15
Rotatable bonds 34
Topological polar surface area 599.73
Molecular weight 1446.36
XLogP -2.39
No. Lipinski's rules broken 3

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
Click here for help

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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

✖
Canonical SMILES OCC1OC(OC2CC(CC(C2OC2OC(C)C(C(C2O)O)O)NC(=O)c2cc(=O)[nH]c(=O)[nH]2)C(=O)NCCNC(=O)COCCOCC(=O)Nc2cc(cc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)C(C(C1O)OC(C(=O)O)CC1CCCCC1)OC(=O)c1ccccc1
Isomeric SMILES OC[C@H]1O[C@@H](O[C@@H]2C[C@@H](C[C@@H]([C@H]2O[C@@H]2O[C@@H](C)[C@H]([C@H]([C@@H]2O)O)O)NC(=O)c2cc(=O)[nH]c(=O)[nH]2)C(=O)NCCNC(=O)COCCOCC(=O)Nc2cc(cc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)[C@@H]([C@H]([C@H]1O)O[C@H](C(=O)O)CC1CCCCC1)OC(=O)c1ccccc1
InChI InChI=1S/C58H74N6O31S3/c1-27-45(69)47(71)48(72)56(90-27)95-49-35(62-53(74)36-23-41(66)64-58(78)63-36)19-31(20-37(49)92-57-51(94-55(77)29-10-6-3-7-11-29)50(46(70)39(24-65)93-57)91-38(54(75)76)16-28-8-4-2-5-9-28)52(73)60-13-12-59-42(67)25-88-14-15-89-26-43(68)61-34-21-32(96(79,80)81)17-30-18-33(97(82,83)84)22-40(44(30)34)98(85,86)87/h3,6-7,10-11,17-18,21-23,27-28,31,35,37-39,45-51,56-57,65,69-72H,2,4-5,8-9,12-16,19-20,24-26H2,1H3,(H,59,67)(H,60,73)(H,61,68)(H,62,74)(H,75,76)(H,79,80,81)(H,82,83,84)(H,85,86,87)(H2,63,64,66,78)/t27-,31+,35-,37+,38-,39+,45+,46-,47+,48-,49+,50-,51+,56-,57+/m0/s1
InChI Key VXBNTHRZPJLRSS-PTCSXESPSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Bioactivity Comments
We do not include the selectins as molecular targets in this database.
Rivipansel is reported in inhibit the binding of E-selection (to sLea or sLex) with an IC50 of 4.3µM. IC50s for inhibition of P-selectin and L-selectin binding are lower, at 423 and 337µM respectively [1].
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
selectin P (CD62) Hs Inhibitor Binding 3.4 pIC50 - 1
⤷ pIC50 3.4 (IC50 4.23x10-4 M) [1]