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 
  • R-Value Observed: 0.193 

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, 4X1Y, 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chainA, C451Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWZ0 (Ovis aries)
Explore D0VWZ0 
Go to UniProtKB:  D0VWZ0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB, D445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E142Rattus norvegicusMutation(s): 2 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3WV
Query on 3WV

Download Ideal Coordinates CCD File 
J [auth B], O [auth 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
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A], K [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
H [auth B], M [auth D]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
LOC
Query on LOC

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

Download Ideal Coordinates CCD File 
G [auth A], L [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LOCIC50:  3790   nM  BindingDB
LOCIC50:  4168.68994140625   nM  BindingDB
LOCKi:  780   nM  BindingDB
LOCKi:  5750   nM  BindingDB
LOCIC50:  6.699999809265137   nM  BindingDB
LOCIC50:  1060   nM  BindingDB
LOCIC50:  2620   nM  BindingDB
LOCIC50:  2400   nM  BindingDB
LOCIC50:  2680   nM  BindingDB
LOCIC50:  800   nM  BindingDB
LOCIC50:  3500   nM  BindingDB
LOCIC50:  10000   nM  BindingDB
LOCIC50:  6930   nM  BindingDB
LOCIC50:  7850   nM  BindingDB
LOCIC50:  2100   nM  BindingDB
LOCKi:  1.600000023841858   nM  BindingDB
LOCKd:  3700   nM  BindingDB
LOCIC50:  29300   nM  BindingDB
LOCIC50:  1400   nM  BindingDB
LOCIC50:  1500   nM  BindingDB
LOCKi:  2500   nM  BindingDB
LOCIC50:  1700   nM  BindingDB
LOCIC50:  1900   nM  BindingDB
LOCIC50:  1260   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.61α = 90
b = 127.86β = 90
c = 255.04γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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