Molecular Playground/YKL-40

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One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.


YKL-40, a Secreted Glycoprotein

Crystal Structure of YKL-40
Crystal Structure of YKL-40

PDB ID 1hjx

Drag the structure with the mouse to rotate
Chitinase-3-like protein 1 complex with glycerol and sulfate, 1hjx
Ligands: , ,
Related: 1hjv, 1hjw, 1la7
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml

YKL-40 is named for its first three amino acid residues--tyrosine, lysine, and leucine-- and its molecular weight, 40 kDa. It is a member of the chitinase family of proteins, although it has no chitinase activity. It has been implicated in the progession of inflammatory diseases, diabetes, and many cancers. It is one of the most up-regulated genes in glioblastoma multiform (GBM), the most common malignacy of the brain and central nervous system. High YKL-40 serum levels correlate with the worst prognosis for many cancers, especially in GBM. It is thought to increase tumor angiogenesis and endothelial cell migration into tumors.

Click here for a stick representation of the ligands bound to YKL-40 (Glycerol, N-ACETYL-D-GLUCOSAMINE, SULFATE ION):

3D structures of YKL-40

Chitinase-3-like protein 1

Additional Resources

For additional information, see: Diabetes & Hypoglycemia
For additional information, see: Cancer


1.) Houston, D.R., Recklies, A.D., Krupa, J.C.,Van Aalten, D.M.F. Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.(2003) J.Biol.Chem. 278: 30206.

2.) Shao et al. YKL-40, a secreted glycoprotein, promotes tumor angiogenesis. Oncogene (2009) 28, 4456–4468.

Molecular Playground banner: YKL-40, A New Cancer Biomarker

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