4X1Y

Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of cytotoxic dolastatin 10 analogues with N-terminal modifications.

Maderna, A.Doroski, M.Subramanyam, C.Porte, A.Leverett, C.A.Vetelino, B.C.Chen, Z.Risley, H.Parris, K.Pandit, J.Varghese, A.H.Shanker, S.Song, C.Sukuru, S.C.Farley, K.A.Wagenaar, M.M.Shapiro, M.J.Musto, S.Lam, M.H.Loganzo, F.O'Donnell, C.J.

(2014) J.Med.Chem. 57: 10527-10543

  • DOI: 10.1021/jm501649k
  • Primary Citation of Related Structures:  4X1I, 4X1K, 4X20

  • PubMed Abstract: 
  • Auristatins, synthetic analogues of the antineoplastic natural product Dolastatin 10, are ultrapotent cytotoxic microtubule inhibitors that are clinically used as payloads in antibody-drug conjugates (ADCs). The design and synthesis of several new au ...

    Auristatins, synthetic analogues of the antineoplastic natural product Dolastatin 10, are ultrapotent cytotoxic microtubule inhibitors that are clinically used as payloads in antibody-drug conjugates (ADCs). The design and synthesis of several new auristatin analogues with N-terminal modifications that include amino acids with α,α-disubstituted carbon atoms are described, including the discovery of our lead auristatin, PF-06380101. This modification of the peptide structure is unprecedented and led to analogues with excellent potencies in tumor cell proliferation assays and differential ADME properties when compared to other synthetic auristatin analogues that are used in the preparation of ADCs. In addition, auristatin cocrystal structures with tubulin are being presented that allow for the detailed examination of their binding modes. A surprising finding is that all analyzed analogues have a cis-configuration at the Val-Dil amide bond in their functionally relevant tubulin bound state, whereas in solution this bond is exclusively in the trans-configuration. This remarkable observation shines light onto the preferred binding mode of auristatins and serves as a valuable tool for structure-based drug design.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, Oncology, Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha chain
A, C
451Ovis ariesN/A
Find proteins for D0VWZ0 (Ovis aries)
Go to UniProtKB:  D0VWZ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D
445Ovis ariesN/A
Find proteins for D0VWY9 (Ovis aries)
Go to UniProtKB:  D0VWY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
142Rattus norvegicusGene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LOC
Query on LOC

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Download CCD File 
B, D
N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
COLCHICINE
C22 H25 N O6
IAKHMKGGTNLKSZ-INIZCTEOSA-N
 Ligand Interaction
3WV
Query on 3WV

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Download CCD File 
B, D
N,2-dimethyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide
C38 H63 N5 O8
ZNENPPNSQVNMCG-BZXSYZDRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LOCKi: 780 - 2500 nM (99) BINDINGDB
LOCIC50: 800 - 4168.7 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.610α = 90.00
b = 127.860β = 90.00
c = 255.040γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
BUSTERphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-25 
  • Released Date: 2015-03-25 
  • Deposition Author(s): Parris, K.D.

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Non-polymer description