24PT | pdb_000024pt

SB225002 with Tubulin

PDB DOI: https://doi.org/10.2210/pdb24PT/pdb

Classification: PROTEIN BINDING
Organism(s): Sus scrofa, Mus musculus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-16 Released: 2026-10-28
Deposition Author(s): Guo, C.Y., Liu, X.Y., Lei, D.S., Wang, Y.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Sichuan Science and Technology Program

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.254 (Depositor), 0.257 (DCC)
R-Value Work:
0.193 (Depositor), 0.199 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Microtubule destabilization by SB225002 through preferential weakening of lateral tubulin interactions revealed by structural and computational analyses

Liu, X.Y., Guo, C.Y., Wang, Y.X., Lei, D.S.

(2026) Journal Of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2026.113625

Macromolecule Content

Total Structure Weight: 260.55 kDa
Atom Count: 17,684
Modeled Residue Count: 2,161
Deposited Residue Count: 2,269
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1B chain	A [auth B], C [auth D]	440	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B [auth C], D [auth E]	431	Sus scrofa	Mutation(s): 0 Gene Names: TUBB2B
UniProt
Find proteins for A0A8D0VN39 (Sus scrofa) Explore A0A8D0VN39 Go to UniProtKB: A0A8D0VN39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D0VN39
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E [auth F]	143	Mus musculus	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63042
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin--tyrosine ligase	F [auth G]	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus) Explore A0A8V0Z8P0 Go to UniProtKB: A0A8V0Z8P0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain G [auth B] MOL2 format, chain R [auth D] MOL2 format, chain G [auth B] mmCIF format, chain R [auth D] mmCIF format, chain G [auth B]	G [auth B], R [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Focus chain R [auth D] Interactions & Density Focus chain G [auth B] Focus chain R [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain Z [auth G]	Z [auth G]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Z [auth G] Interactions & Density Focus chain Z [auth G]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain K [auth C] MOL2 format, chain W [auth E] MOL2 format, chain K [auth C] mmCIF format, chain W [auth E] mmCIF format, chain K [auth C]	K [auth C], W [auth E]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth C] Focus chain W [auth E] Interactions & Density Focus chain K [auth C] Focus chain W [auth E]
A1E64( Subject of Investigation/LOI) Query on A1E64 Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C]	N [auth C], O [auth C], U [auth D], X [auth E]	1-(2-bromophenyl)-3-(4-nitro-2-oxidanyl-phenyl)urea C₁₃ H₁₀ Br N₃ O₄ MQBZVUNNWUIPMK-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain U [auth D] Focus chain X [auth E]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain M [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth C]	M [auth C], Q [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain Q [auth C] Interactions & Density Focus chain M [auth C] Focus chain Q [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain H [auth B] MOL2 format, chain T [auth D] MOL2 format, chain H [auth B] mmCIF format, chain T [auth D] mmCIF format, chain H [auth B]	H [auth B], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain T [auth D] Interactions & Density Focus chain H [auth B] Focus chain T [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain V [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain V [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain V [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain J [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain J [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain J [auth B]	J [auth B], P [auth C], S [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain Y [auth E] Interactions & Density Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254 (Depositor), 0.257 (DCC)
R-Value Work: 0.193 (Depositor), 0.199 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.685	α = 90
b = 157.35	β = 90
c = 180.637	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171300
National Natural Science Foundation of China (NSFC)	China	82473782
Sichuan Science and Technology Program	China	2025ZNSFSC0687