9FYD image
Deposition Date 2024-07-03
Release Date 2024-10-09
Last Version Date 2024-12-11
Entry Detail
PDB ID:
9FYD
Keywords:
Title:
tubulin - cryptophycin-uD[Dab] complex
Biological Source:
Source Organism:
Rattus norvegicus (Taxon ID: 10116)
Gallus gallus (Taxon ID: 9031)
Bos taurus (Taxon ID: 9913)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin alpha-1B chain
Chain IDs:A, C
Chain Length:451
Number of Molecules:2
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin beta-2B chain
Gene (Uniprot):TUBB2B
Chain IDs:B, D
Chain Length:445
Number of Molecules:2
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Stathmin-4
Gene (Uniprot):Stmn4
Chain IDs:E
Chain Length:143
Number of Molecules:1
Biological Source:Rattus norvegicus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin tyrosine ligase
Gene (Uniprot):TTL
Chain IDs:F
Chain Length:384
Number of Molecules:1
Biological Source:Gallus gallus
Primary Citation
Highly Cytotoxic Cryptophycin Derivatives with Modification in Unit D for Conjugation.
Angew.Chem.Int.Ed.Engl. 63 e202416210 e202416210 (2024)
PMID: 39324938 DOI: 10.1002/anie.202416210

Abstact

Cytotoxic payloads for drug conjugates suitable for directed tumor therapy need to be highly potent and require a functional group for conjugation with the homing device (antibody, peptide, or small molecule). Cryptophycins are cyclodepsipeptides that stand out from the realm of natural products due to their extraordinarily high cytotoxicity. However, the installation of a suitable conjugation handle without compromising the toxicity is highly challenging. The unit D, natively 2-hydroxyisocaproic acid (leucic acid), was envisaged as a promising attachment site based on structural information from X-ray analysis. A versatile, scalable and efficient synthetic route towards conjugable cryptophycins with modification in unit D was developed and an array of new cryptophycin analogues was synthesized. Several derivatives, especially those containing lipophilic groups with low steric demand such as alkylated amino groups, exhibit low picomolar cytotoxicity often combined with efficacy against multidrug-resistant tumor cells. The newly established cryptophycin analogues comprise a broad range of relevant functional groups used as conjugation handles, among them amino, hydroxy, carboxy, as well as sulfur-containing derivatives. X-ray crystallographic analysis of a tubulin-bound cryptophycin together with quantitative structure activity relationship manifested rationales for the synthesis of most potent cryptophycin derivatives and further confirmed the suitability of modifications in unit D.

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Primary Citation of related structures
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