6Y4N

Structure of Tubulin Tyrosine Ligase in Complex with Tb116


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis.

Nicolaou, K.C.Pan, S.Pulukuri, K.K.Ye, Q.Rigol, S.Erande, R.D.Vourloumis, D.Nocek, B.P.Munneke, S.Lyssikatos, J.Valdiosera, A.Gu, C.Lin, B.Sarvaiaya, H.Trinidad, J.Sandoval, J.Lee, C.Hammond, M.Aujay, M.Taylor, N.Pysz, M.Purcell, J.W.Gavrilyuk, J.

(2021) J Org Chem 86: 3377-3421

  • DOI: https://doi.org/10.1021/acs.joc.0c02755
  • Primary Citation of Related Structures:  
    6Y4M, 6Y4N

  • PubMed Abstract: 

    Molecular design, synthesis, and biological evaluation of tubulysin analogues, linker-drugs, and antibody-drug conjugates are described. Among the new discoveries reported is the identification of new potent analogues within the tubulysin family that carry a C11 alkyl ether substituent, rather than the usual ester structural motif at that position, a fact that endows the former with higher plasma stability than that of the latter. Also described herein are X-ray crystallographic analysis studies of two tubulin-tubulysin complexes formed within the α/β interface between two tubulin heterodimers and two highly potent tubulysin analogues, one of which exhibited a different binding mode to the one previously reported for tubulysin M. The X-ray crystallographic analysis-derived new insights into the binding modes of these tubulysin analogues explain their potencies and provide inspiration for further design, synthesis, and biological investigations within this class of antitumor agents. A number of these analogues were conjugated as payloads with appropriate linkers at different sites allowing their attachment onto targeting antibodies for cancer therapies. A number of such antibody-drug conjugates were constructed and tested, both in vivo and in vitro, leading to the identification of at least one promising ADC (Herceptin- LD3 ), warranting further investigations.


  • Organizational Affiliation

    Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63043
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin-Tyrosine Ligase384Gallus gallusMutation(s): 0 
Gene Names: TTL
Entity Groups  
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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G [auth A],
P [auth C],
V [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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Y [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

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J [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
O9K
Query on O9K

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N [auth B][(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate
C13 H20 N2 O3 S
QIMGLCHKHZYHQD-VXGBXAGGSA-N
O9N
Query on O9N

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O [auth B]methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate
C12 H18 N2 O2
GXDWYXRQHBMHOS-QWRGUYRKSA-N
MES
Query on MES

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L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
P6S
Query on P6S

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U [auth C]benzyl hydrogen carbonate
C8 H8 O3
NJAPCAIWQRPQPY-UHFFFAOYSA-N
PGE
Query on PGE

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S [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
O9B
Query on O9B

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M [auth B](2~{R})-1-methylpiperidine-2-carboxylic acid
C7 H13 N O2
BPSLZWSRHTULGU-ZCFIWIBFSA-N
VAL
Query on VAL

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T [auth C]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
PEG
Query on PEG

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X [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

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I [auth A],
R [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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H [auth A],
K [auth B],
Q [auth C],
W [auth D],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.284α = 90
b = 154.969β = 90
c = 183.433γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection