5GON | pdb_00005gon

Structures of a beta-lactam bridged analogue in complex with tubulin

PDB DOI: https://doi.org/10.2210/pdb5GON/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2016-07-28 Released: 2017-03-22
Deposition Author(s): Zhou, L., Liu, Y., Cheng, L., Wang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.257 (Depositor), 0.256 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Potent Antitumor Activities and Structure Basis of the Chiral beta-Lactam Bridged Analogue of Combretastatin A-4 Binding to Tubulin.

Zhou, P., Liu, Y., Zhou, L., Zhu, K., Feng, K., Zhang, H., Liang, Y., Jiang, H., Luo, C., Liu, M., Wang, Y.

(2016) J Med Chem 59: 10329-10334

PubMed: 27805821 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.6b01268
Primary Citation Related Structures:
5GON

PubMed Abstract:
A series of chiral β-lactam bridged analogues (3-substituted 1,4-diaryl-2-azetidinones) of combretastatin A-4 (CA-4) were synthesized asymmetrically, and their antitumor activities were evaluated in vitro and in vivo. The cocrystal structure of tubulin in complex with compound 9 was determined by X-ray crystallography, which showed that 9 binds to the same site as colchicine with similar binding mode, and the absolute configuration of its C-4 was first identified and demonstrated to be critically important for their antiproliferative activities.

Organizational Affiliation

School of Pharmacy, Fudan University , Shanghai 201203, China.

Macromolecule Content

Total Structure Weight: 258.4 kDa
Atom Count: 17,847
Modeled Residue Count: 2,162
Deposited Residue Count: 2,256
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	440	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	431	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	136	Rattus norvegicus	Mutation(s): 0
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
Uncharacterized protein	F	378	Gallus gallus	Mutation(s): 0 Gene Names: TTL

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 W [auth C] MOL2 format, chain G [auth A] MOL2 format, chain W [auth C] mmCIF format, chain G [auth A] mmCIF format, chain W [auth C]	G [auth A], W [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain W [auth C]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain M [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain M [auth B]	EA [auth D], M [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain EA [auth D] Focus chain M [auth B] Interactions & Density Focus chain EA [auth D] Focus chain M [auth B]
6ZR Query on 6ZR Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	(3R,4R)-4-(4-methoxy-3-oxidanyl-phenyl)-3-methyl-1-(3,4,5-trimethoxyphenyl)azetidin-2-one C₂₀ H₂₃ N O₆ KLFAJLHIJQPMNJ-ADLMAVQZSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] GA [auth D] HA [auth D] I [auth A] J [auth A] AA [auth C], GA [auth D], HA [auth D], I [auth A], J [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], V [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C]	BA [auth C], CA [auth C], DA [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C]	K [auth A], R [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Focus chain U [auth C] Interactions & Density Focus chain K [auth A] Focus chain R [auth B] Focus chain U [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain IA [auth F] SDF format, chain N [auth B] SDF format, chain X [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain X [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain X [auth C]	FA [auth D], H [auth A], IA [auth F], N [auth B], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain H [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain X [auth C] Interactions & Density Focus chain FA [auth D] Focus chain H [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.257 (Depositor), 0.256 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.507	α = 90
b = 156.463	β = 90
c = 181.838	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2024-03-20
Changes: Advisory, Data collection, Database references, Derived calculations