8RIW | pdb_00008riw

T2R-TTL-1-L01 complex

PDB DOI: https://doi.org/10.2210/pdb8RIW/pdb

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

Deposited: 2023-12-19 Released: 2024-03-27
Deposition Author(s): Prota, A.E.P., Boiarska, Z., Homer, J.A., Steinmetz, M.O., Moses, J.E.
Funding Organization(s): European Union (EU), Swiss National Science Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (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

Modular synthesis of functional libraries by accelerated SuFEx click chemistry.

Homer, J.A., Koelln, R.A., Barrow, A.S., Gialelis, T.L., Boiarska, Z., Steinohrt, N.S., Lee, E.F., Yang, W.H., Johnson, R.M., Chung, T., Habowski, A.N., Vishwakarma, D.S., Bhunia, D., Avanzi, C., Moorhouse, A.D., Jackson, M., Tuveson, D.A., Lyons, S.K., Lukey, M.J., Fairlie, W.D., Haider, S.M., Steinmetz, M.O., Prota, A.E., Moses, J.E.

(2024) Chem Sci 15: 3879-3892

PubMed: 38487227 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d3sc05729a
Primary Citation Related Structures:
8RIV, 8RIW

PubMed Abstract:
Accelerated SuFEx Click Chemistry (ASCC) is a powerful method for coupling aryl and alkyl alcohols with SuFEx-compatible functional groups. With its hallmark favorable kinetics and exceptional product yields, ASCC streamlines the synthetic workflow, simplifies the purification process, and is ideally suited for discovering functional molecules. We showcase the versatility and practicality of the ASCC reaction as a tool for the late-stage derivatization of bioactive molecules and in the array synthesis of sulfonate-linked, high-potency, microtubule targeting agents (MTAs) that exhibit nanomolar anticancer activity against multidrug-resistant cancer cell lines. These findings underscore ASCC's promise as a robust platform for drug discovery.

Organizational Affiliation

Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA moses@cshl.edu.

Macromolecule Content

Total Structure Weight: 265.54 kDa
Atom Count: 17,779
Modeled Residue Count: 2,195
Deposited Residue Count: 2,318
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	142	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 tyrosine ligase	F	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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain G [auth A]	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 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 L [auth B] MOL2 format, chain W [auth D] MOL2 format, chain L [auth B] mmCIF format, chain W [auth D] mmCIF format, chain L [auth B]	L [auth B], W [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain W [auth D] Interactions & Density Focus chain L [auth B] Focus chain W [auth D]
A1H00 (Subject of Investigation/LOI) Query on A1H00 Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain P [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain P [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain P [auth B]	P [auth B], Y [auth D]	(2-methyl-1~{H}-indol-5-yl) 3,4,5-trimethoxybenzenesulfonate C₁₈ H₁₉ N O₆ S VOTVHPZHTCCWTA-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Y [auth D] Interactions & Density Focus chain P [auth B] Focus chain Y [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	K [auth A], Q [auth B], R [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	I [auth A], J [auth A], N [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain U [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain AA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain AA [auth F]	AA [auth F], H [auth A], M [auth B], T [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.687	α = 90
b = 156.104	β = 90
c = 182.528	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union (EU)	European Union	860070 TubInTrain
Swiss National Science Foundation	Switzerland	310030_192566
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5P30CA045508
Australian Research Council (ARC)	Australia	FT170100156