8C0F | pdb_00008c0f

Tubulin-PTC596 complex

PDB DOI: https://doi.org/10.2210/pdb8C0F/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-16 Released: 2022-12-28
Deposition Author(s): Prota, A.E., Muehlethaler, T., Weetall, M., Steinmetz, M.O.
Funding Organization(s): Wellcome Trust, Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Preclinical and Early Clinical Development of PTC596, a Novel Small-Molecule Tubulin-Binding Agent

Jernigan, F., Branstrom, A., Baird, J.D., Cao, L., Dali, M., Furia, B., Kim, M.J., O'Keefe, K., Kong, R., Laskin, O.L., Colacino, J.M., Pykett, M., Mollin, A., Sheedy, J., Dumble, M., Moon, Y.-C., Sheridan, R., Muehlethaler, T., Spiegel, R.J., Prota, A.E., Steinmetz, M.O., Weetall, M.

(2021) Mol Cancer Ther 20: 1846-1857

PubMed: 34315764 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1158/1535-7163.MCT-20-0774
Primary Citation Related Structures:
8C0F

PubMed Abstract:
PTC596 is an investigational small-molecule tubulin-binding agent. Unlike other tubulin-binding agents, PTC596 is orally bioavailable and is not a P-glycoprotein substrate. So as to characterize PTC596 to position the molecule for optimal clinical development, the interactions of PTC596 with tubulin using crystallography, its spectrum of preclinical in vitro anticancer activity, and its pharmacokinetic-pharmacodynamic relationship were investigated for efficacy in multiple preclinical mouse models of leiomyosarcomas and glioblastoma. Using X-ray crystallography, it was determined that PTC596 binds to the colchicine site of tubulin with unique key interactions. PTC596 exhibited broad-spectrum anticancer activity. PTC596 showed efficacy as monotherapy and additive or synergistic efficacy in combinations in mouse models of leiomyosarcomas and glioblastoma. PTC596 demonstrated efficacy in an orthotopic model of glioblastoma under conditions where temozolomide was inactive. In a first-in-human phase I clinical trial in patients with cancer, PTC596 monotherapy drug exposures were compared with those predicted to be efficacious based on mouse models. PTC596 is currently being tested in combination with dacarbazine in a clinical trial in adults with leiomyosarcoma and in combination with radiation in a clinical trial in children with diffuse intrinsic pontine glioma.

Organizational Affiliation

PTC Therapeutics, Inc., South Plainfield, New Jersey.

Macromolecule Content

Total Structure Weight: 265.48 kDa
Atom Count: 18,221
Modeled Residue Count: 2,180
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain G [auth A]	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain Z [auth F]	Z [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Z [auth F] Interactions & Density Focus chain Z [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain J [auth B] MOL2 format, chain W [auth D] MOL2 format, chain J [auth B] mmCIF format, chain W [auth D] mmCIF format, chain J [auth B]	J [auth B], W [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Focus chain W [auth D] Interactions & Density Focus chain J [auth B] Focus chain W [auth D]
SOZ (Subject of Investigation/LOI) Query on SOZ Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	5-fluoranyl-2-(6-fluoranyl-2-methyl-benzimidazol-1-yl)-~{N}4-[4-(trifluoromethyl)phenyl]pyrimidine-4,6-diamine C₁₉ H₁₃ F₅ N₆ TWLWOOPCEXYVBE-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B]	M [auth B], R [auth C], S [auth C], T [auth C], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain Y [auth E]	Y [auth E]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Y [auth E] Interactions & Density Focus chain Y [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain I [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth A]	I [auth A], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain AA [auth F] MOL2 format, chain X [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain AA [auth F]	AA [auth F], H [auth A], K [auth B], P [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain X [auth D]