6LSM

Tubulin Polymerization Inhibitors

PDB DOI: https://doi.org/10.2210/pdb6LSM/pdb

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

Deposited: 2020-01-17 Released: 2021-01-20
Deposition Author(s): Gang, L., Wang, Y.X., Chen, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.227
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Design, Synthesis, and Bioevaluation of Pyrazolo[1,5-a]Pyrimidine Derivatives as Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site with Potent Anticancer Activities

Gang, L., Wang, Y.X., Chen, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 264.85 kDa
Atom Count: 17,751
Modelled Residue Count: 2,200
Deposited Residue Count: 2,317
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	450	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Sus scrofa	Mutation(s): 0 Gene Names: TUBB2B
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63042
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 G [auth A] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain S [auth C]	G [auth A], S [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F]	Y [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain V [auth D] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D]	L [auth B], V [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain V [auth D]
ERX (Subject of Investigation/LOI) Query on ERX Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	2-(4-methylphenyl)-7-(3,4,5-trimethoxyphenyl)pyrazolo[1,5-a]pyrimidine C₂₂ H₂₁ N₃ O₃ JSNTVTRKXKWPFD-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	O [auth B], P [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C]	I [auth A], K [auth A], N [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain U [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth F]	H [auth A] M [auth B] Q [auth B] T [auth C] W [auth D] H [auth A], M [auth B], Q [auth B], T [auth C], W [auth D], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth F]