5KX5

Crystal structure of tubulin-stathmin-TTL-Compound 11 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, Synthesis, and Cytotoxic Evaluation of Novel Tubulysin Analogues as ADC Payloads.

Leverett, C.A.Sukuru, S.C.Vetelino, B.C.Musto, S.Parris, K.Pandit, J.Loganzo, F.Varghese, A.H.Bai, G.Liu, B.Liu, D.Hudson, S.Doppalapudi, V.R.Stock, J.O'Donnell, C.J.Subramanyam, C.

(2016) ACS Med Chem Lett 7: 999-1004

  • DOI: 10.1021/acsmedchemlett.6b00274

  • PubMed Abstract: 
  • The tubulysin class of natural products has attracted much attention from the medicinal chemistry community due to its potent cytotoxicity against a wide range of human cancer cell lines, including significant activity in multidrug-resistant carcinom ...

    The tubulysin class of natural products has attracted much attention from the medicinal chemistry community due to its potent cytotoxicity against a wide range of human cancer cell lines, including significant activity in multidrug-resistant carcinoma models. As a result of their potency, the tubulysins have become an important tool for use in targeted therapy, being widely pursued as payloads in the development of novel small molecule drug conjugates (SMDCs) and antibody-drug conjugates (ADCs). A structure-based and parallel medicinal chemistry approach was applied to the synthesis of novel tubulysin analogues. These efforts led to the discovery of a number of novel and potent cytotoxic tubulysin analogues, providing a framework for our simultaneous report, which highlights the discovery of tubulysin-based ADCs, including use of site-specific conjugation to address in vivo stability of the C-11 acetate functionality.


    Organizational Affiliation

    Oncology R&D, Pfizer Worldwide R&D , Pearl River, New York 10965, United States.,Medicinal Sciences, Pfizer Worldwide R&D , Groton, Connecticut 06340, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha chain
A, C
451Ovis ariesMutation(s): 0 
Find proteins for D0VWZ0 (Ovis aries)
Go to UniProtKB:  D0VWZ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D
445Ovis ariesMutation(s): 0 
Find proteins for D0VWY9 (Ovis aries)
Go to UniProtKB:  D0VWY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TTL protein
F
384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Go to Gene View: TTL
Go to UniProtKB:  E1BQ43
Small Molecules
Ligands 6 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
ADP
Query on ADP

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Download CCD File 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-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
CA
Query on CA

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Download CCD File 
A, B, C, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
6YK
Query on 6YK

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Download CCD File 
B, D
(2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,2-dimethylpyrrolidin-2-yl]carbonylamino]-3-methyl-pentanoyl]-methyl-amino]-4-methyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-aminophenyl)-2-methyl-pentanoic acid
C38 H58 N6 O7 S
YYYFRRSYTVJIOE-WWAIPBPMSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.790α = 90.00
b = 153.900β = 90.00
c = 185.200γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-20 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Parris, K.

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release