6K9V

Crystal structure of tubulin in complex with inhibitor D64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.543 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the design of indole derivatives as tubulin polymerization inhibitors.

Li, Y.Yang, J.Niu, L.Hu, D.Li, H.Chen, L.Yu, Y.Chen, Q.

(2019) Febs Lett. --: --

  • DOI: 10.1002/1873-3468.13566

  • PubMed Abstract: 
  • Microtubules are composed of αβ-tubulin heterodimers, and drugs that interfere with microtubule dynamics are used widely in cancer chemotherapy. Small synthetic molecules with an indole nucleus as a core structure have been identified as microtubule ...

    Microtubules are composed of αβ-tubulin heterodimers, and drugs that interfere with microtubule dynamics are used widely in cancer chemotherapy. Small synthetic molecules with an indole nucleus as a core structure have been identified as microtubule inhibitors and recognized as anticancer agents. However, structural information for the interactions between indole derivatives and tubulin is sparse. Here, we present the 2.55 Å crystal structure of tubulin in complex with the indole derivative D64131. We compare the binding modes of D64131, colchicine, and five other indole derivatives to tubulin. These results reveal the interactions between the indole derivatives and tubulin, explain previous results of structure-activity-relationship (SAR) studies and, thus, provide insights into the development of new indole derivatives targeting the colchicine binding site.


    Organizational Affiliation

    Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C
450Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
Go to UniProtKB:  P81947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B, D
445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Go to Gene View: TUBB2B
Go to UniProtKB:  Q6B856
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
Tubulin tyrosine ligase
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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
D3L
Query on D3L

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Download CCD File 
B, D
(5-methoxy-1H-indol-2-yl)-phenyl-methanone
C16 H13 N O2
ICMIJSRDISNKOC-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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

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C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

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Download CCD File 
F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.543 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.219α = 90.00
b = 157.435β = 90.00
c = 180.045γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-18 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Yu, Y., Chen, Q.

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release