7EXC

Crystal structure of T2R-TTL-1129A2 complex

PDB DOI: https://doi.org/10.2210/pdb7EXC/pdb

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

Deposited: 2021-05-26 Released: 2022-06-01
Deposition Author(s): Yang, J.H., Yan, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.264
R-Value Work: 0.218
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-Based Design and Synthesis of N-Substituted 3-Amino-beta-Carboline Derivatives as Potent alpha beta-Tubulin Degradation Agents

Li, Y., Liu, Y., Zhu, Z., Yan, W., Zhang, C., Yang, Z., Bai, P., Tang, M., Shi, M., He, W., Fu, S., Liu, J., Han, K., Li, J., Xie, L., Ye, H., Yang, J., Chen, L.

(2022) J Med Chem 65: 2675-2693

DOI: https://doi.org/10.1021/acs.jmedchem.1c02159

Macromolecule Content

Total Structure Weight: 270.53 kDa
Atom Count: 18,047
Modelled Residue Count: 2,184
Deposited Residue Count: 2,365
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	451	Sus scrofa	Mutation(s): 0
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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Sus scrofa	Mutation(s): 0
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	189	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
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 O [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D]	G [auth A], O [auth C], R [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth C] Focus chain R [auth D]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F]	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
JEL (Subject of Investigation/LOI) Query on JEL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain S [auth D] MOL2 format, chain M [auth B] MOL2 format, chain S [auth D]	M [auth B], S [auth D]	N-[[3-(1,3-benzodioxol-5-yloxy)phenyl]methyl]-9H-pyrido[3,4-b]indol-3-amine C₂₅ H₁₉ N₃ O₃ AGUNDEAVRTZOAH-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain S [auth D] Interactions & Density Focus chain M [auth B] Focus chain S [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 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 J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth C]	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 H [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	H [auth A], K [auth B], P [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]