7CNM

YDX in complex with tubulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design.

Chengyong, W.Jinghong, X.Yanyan, W.Qing-Jie, X.Lingling, M.Yuyan, L.Hai, C.Qian, L.Quan, Z.Bo, S.Yuxi, W.

(2021) FEBS Lett 595: 195-205

  • DOI: https://doi.org/10.1002/1873-3468.14003
  • Primary Citation of Related Structures:  
    7CNM, 7CNN, 7CNO

  • PubMed Abstract: 

    Tubulin vinca-domain ligands can inhibit microtubule polymerization, causing cell death in mitosis, and their potential against multiple cancer types has been demonstrated. However, due to drug resistance and toxicities, development of novel vinca-domain ligands is still needed. In this study, we determined the high-resolution crystal structures of vinorelbine, YXD, and Phomopsin A in complex with tubulin at 2.5 Å. Additionally, we recapitulated all previously published high-resolution crystal structures of the vinca binding site to reveal critical residues and the molecular mechanism of vinca-domain ligands interacting with tubulin. Furthermore, we designed putatively novel triazolopyrimidine derivatives by introducing secondary amine groups to establish salt-bridge and H-bond interactions with Asp179 β1 and Asn329 α2 . Our studies provided the structural basis for designing novel tubulin vinca-domain ligands.


  • Organizational Affiliation

    Cancer Center, West China Hospital, Sichuan University, Chengdu, China.


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  
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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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UniProt GroupP02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Mus musculusMutation(s): 0 
Gene Names: Stmn4
UniProt & NIH Common Fund Data Resources
Find proteins for P63042 (Mus musculus)
Explore P63042 
Go to UniProtKB:  P63042
IMPC:  MGI:1931224
Entity Groups  
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UniProt GroupP63042
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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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G70 (Subject of Investigation/LOI)
Query on G70

Download Ideal Coordinates CCD File 
N [auth B],
T [auth D]
(2~{S},4~{S})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-4-methyl-3-[[(2~{S},3~{S})-3-methyl-2-[[(2~{R})-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-cyclohexyl-2-methyl-pentanoic acid
C37 H61 N5 O7 S
DJCPPKXNIHCSPF-UZNIZVIGSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

Download Ideal Coordinates CCD File 
U [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
J [auth B],
S [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B],
R [auth C]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA
Query on CA

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

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
P [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.127α = 90
b = 155.022β = 90
c = 186.278γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description