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D13-9001   Click here for help

GtoPdb Ligand ID: 14442

Synonyms: ABI-PP
PDB Ligand
Compound class: Synthetic organic
Comment: D13-9001 is a pyridopyrimidine derivative that acts as a bacterial efflux pump inhibitor (EPI) [2]. EPIs have potential clinical utility as adjunctive therapeutic agents for the treatment of infections caused by Gram-negative pathogens.
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 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.

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Hydrogen bond acceptors 16
Hydrogen bond donors 3
Rotatable bonds 15
Topological polar surface area 230.24
Molecular weight 693.78
XLogP 0.51
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
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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.

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/)

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Canonical SMILES CC(C)(C)C1=CSC(=N1)NC(=O)C2=CC3=NC(=C(/C=C/C4=NNN=N4)C(=O)N3C=C2)N5CCC[C@H](C5)OC(=O)NCC[N+](C)(C)CC(=O)[O-]
Isomeric SMILES CC(C)(C)C1=CSC(=N1)NC(=O)C2=CC3=NC(=C(C(=O)N3C=C2)/C=C/C4=NNN=N4)N5CCC[C@H](C5)OC(=O)NCC[N+](C)(C)CC(=O)[O-]
InChI InChI=1S/C31H39N11O6S/c1-31(2,3)22-18-49-29(33-22)35-27(45)19-10-13-41-24(15-19)34-26(21(28(41)46)8-9-23-36-38-39-37-23)40-12-6-7-20(16-40)48-30(47)32-11-14-42(4,5)17-25(43)44/h8-10,13,15,18,20H,6-7,11-12,14,16-17H2,1-5H3,(H3-,32,33,35,36,37,38,39,43,44,45,47)/t20-/m1/s1
InChI Key RVJNIKFVEAWLQC-HXUWFJFHSA-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/)
References
1. Nakashima R, Sakurai K, Yamasaki S, Hayashi K, Nagata C, Hoshino K, Onodera Y, Nishino K, Yamaguchi A. (2013)
Structural basis for the inhibition of bacterial multidrug exporters.
Nature, 500 (7460): 102-6. [PMID:23812586]
2. Yoshida K, Nakayama K, Ohtsuka M, Kuru N, Yokomizo Y, Sakamoto A, Takemura M, Hoshino K, Kanda H, Nitanai H et al.. (2007)
MexAB-OprM specific efflux pump inhibitors in Pseudomonas aeruginosa. Part 7: highly soluble and in vivo active quaternary ammonium analogue D13-9001, a potential preclinical candidate.
Bioorg Med Chem, 15 (22): 7087-97. [PMID:17869116]
3. Zuo Z, Weng J, Wang W. (2016)
Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations.
J Phys Chem B, 120 (9): 2145-54. [PMID:26900716]