muramyl dipeptide   Click here for help

GtoPdb Ligand ID: 5024

Abbreviated name: MDP
PDB Ligand
Compound class: Natural product
Comment: Muramyl dipeptide (MDP) is the minimal bioactive peptidoglycan motif common to all bacteria. It is a ligand for the NOD2 pattern recognition receptor [1,3].
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 15
Hydrogen bond donors 8
Rotatable bonds 15
Topological polar surface area 246.84
Molecular weight 492.21
XLogP -3.78
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(O)C(C(C1O)OC(C(=O)NC(C(=O)NC(C(=O)N)CCC(=O)O)C)C)NC(=O)C
Isomeric SMILES OC[C@H]1O[C@@H](O)[C@@H]([C@H]([C@@H]1O)O[C@@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N)CCC(=O)O)C)C)NC(=O)C
InChI InChI=1S/C19H32N4O11/c1-7(17(30)23-10(16(20)29)4-5-12(26)27)21-18(31)8(2)33-15-13(22-9(3)25)19(32)34-11(6-24)14(15)28/h7-8,10-11,13-15,19,24,28,32H,4-6H2,1-3H3,(H2,20,29)(H,21,31)(H,22,25)(H,23,30)(H,26,27)/t7-,8+,10+,11+,13+,14+,15+,19+/m0/s1
InChI Key BSOQXXWZTUDTEL-ZUYCGGNHSA-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. Girardin SE, Boneca IG, Viala J, Chamaillard M, Labigne A, Thomas G, Philpott DJ, Sansonetti PJ. (2003)
Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection.
J Biol Chem, 278 (11): 8869-72. [PMID:12527755]
2. Hu Y, Song F, Jiang H, Nuñez G, Smith DE. (2018)
SLC15A2 and SLC15A4 Mediate the Transport of Bacterially Derived Di/Tripeptides To Enhance the Nucleotide-Binding Oligomerization Domain-Dependent Immune Response in Mouse Bone Marrow-Derived Macrophages.
J Immunol, 201 (2): 652-662. [PMID:29784761]
3. Inohara N, Ogura Y, Fontalba A, Gutierrez O, Pons F, Crespo J, Fukase K, Inamura S, Kusumoto S, Hashimoto M et al.. (2003)
Host recognition of bacterial muramyl dipeptide mediated through NOD2. Implications for Crohn's disease.
J Biol Chem, 278 (8): 5509-12. [PMID:12514169]
4. Ismair MG, Vavricka SR, Kullak-Ublick GA, Fried M, Mengin-Lecreulx D, Girardin SE. (2006)
hPepT1 selectively transports muramyl dipeptide but not Nod1-activating muramyl peptides.
Can J Physiol Pharmacol, 84 (12): 1313-9. [PMID:17487240]
5. Kudo M, Kobayashi-Nakamura K, Kitajima N, Tsuji-Naito K. (2020)
Alternate expression of PEPT1 and PEPT2 in epidermal differentiation is required for NOD2 immune responses by bacteria-derived muramyl dipeptide.
Biochem Biophys Res Commun, 522 (1): 151-156. [PMID:31757425]
6. Ma GG, Shi B, Zhang XP, Qiu Y, Tu GW, Luo Z. (2019)
The pathways and mechanisms of muramyl dipeptide transcellular transport mediated by PepT1 in enterogenous infection.
Ann Transl Med, 7 (18): 473. [PMID:31700909]
7. Nakamura N, Lill JR, Phung Q, Jiang Z, Bakalarski C, de Mazière A, Klumperman J, Schlatter M, Delamarre L, Mellman I. (2014)
Endosomes are specialized platforms for bacterial sensing and NOD2 signalling.
Nature, 509 (7499): 240-4. [PMID:24695226]
8. Song F, Hu Y, Wang Y, Smith DE, Jiang H. (2018)
Functional Characterization of Human Peptide/Histidine Transporter 1 in Stably Transfected MDCK Cells.
Mol Pharm, 15 (2): 385-393. [PMID:29224352]
9. Sun D, Wang Y, Tan F, Fang D, Hu Y, Smith DE, Jiang H. (2013)
Functional and molecular expression of the proton-coupled oligopeptide transporters in spleen and macrophages from mouse and human.
Mol Pharm, 10 (4): 1409-16. [PMID:23442152]
10. Vavricka SR, Musch MW, Chang JE, Nakagawa Y, Phanvijhitsiri K, Waypa TS, Merlin D, Schneewind O, Chang EB. (2004)
hPepT1 transports muramyl dipeptide, activating NF-kappaB and stimulating IL-8 secretion in human colonic Caco2/bbe cells.
Gastroenterology, 127 (5): 1401-9. [PMID:15521010]
11. Wang Y, Hu Y, Li P, Weng Y, Kamada N, Jiang H, Smith DE. (2018)
Expression and regulation of proton-coupled oligopeptide transporters in colonic tissue and immune cells of mice.
Biochem Pharmacol, 148: 163-173. [PMID:29305856]