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- PDB-7yhn: ANTI-TUMOR AGENT Y48 IN COMPLEX WITH TUBULIN -

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Basic information

Entry
Database: PDB / ID: 7yhn
TitleANTI-TUMOR AGENT Y48 IN COMPLEX WITH TUBULIN
Components
  • Stathmin
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / MITOSIS / ANTITUMOR PROTEIN
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site ...Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-IUK / Stathmin-4 / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDu, T. / Ji, M. / Hou, Z. / Lin, S. / Zhang, J. / Wu, D. / Zhang, K. / Lu, D. / Xu, H. / Chen, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2022-I2M-JB-010 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization of Benzamide Derivatives as Potent and Orally Active Tubulin Inhibitors Targeting the Colchicine Binding Site.
Authors: Lin, S. / Du, T. / Zhang, J. / Wu, D. / Tian, H. / Zhang, K. / Jiang, L. / Lu, D. / Sheng, L. / Li, Y. / Ji, M. / Chen, X. / Xu, H.
History
DepositionJul 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,64218
Polymers218,4695
Non-polymers3,17313
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-124 kcal/mol
Surface area64570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.870, 102.030, 131.130
Angle α, β, γ (deg.)90.000, 106.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: sequence mismatches are due to the database error / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein Stathmin


Mass: 18060.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100739720, LOC100155126 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z508

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Non-polymers , 6 types, 35 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-IUK / 4-methyl-3-[(4-methylphenyl)sulfonylamino]-~{N}-[(6-methylpyridin-3-yl)methyl]benzamide / Y48


Mass: 409.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H23N3O3S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% PEG 4000, 8% GLYCEROL, 30MM MAGNESIUM CHLORIDE, 30MM CALCIUM CHLORIDE, 100MM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→78.33 Å / Num. obs: 63088 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 69.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 3167 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LS4

6ls4


Resolution: 2.6→78.33 Å / SU ML: 0.3114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.8579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2723 3208 5.1 %
Rwork0.2299 59652 -
obs0.2321 62860 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13646 0 200 22 13868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005114143
X-RAY DIFFRACTIONf_angle_d0.867519271
X-RAY DIFFRACTIONf_chiral_restr0.04952148
X-RAY DIFFRACTIONf_plane_restr0.00542517
X-RAY DIFFRACTIONf_dihedral_angle_d19.70854983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.42651360.38392601X-RAY DIFFRACTION99.24
2.64-2.680.41021500.38292535X-RAY DIFFRACTION96.76
2.68-2.720.36751300.34322611X-RAY DIFFRACTION99.49
2.72-2.770.35371350.31672559X-RAY DIFFRACTION99.15
2.77-2.820.3771360.2952610X-RAY DIFFRACTION98.95
2.82-2.880.38261350.2972586X-RAY DIFFRACTION99.45
2.88-2.930.35431560.28922584X-RAY DIFFRACTION99.13
2.93-30.3461350.28672575X-RAY DIFFRACTION99.01
3-3.070.38471330.29242600X-RAY DIFFRACTION99.31
3.07-3.140.34161470.30172605X-RAY DIFFRACTION99.28
3.14-3.230.31491280.28952584X-RAY DIFFRACTION98.58
3.23-3.320.35611300.27282576X-RAY DIFFRACTION98.65
3.32-3.430.32621320.25122613X-RAY DIFFRACTION98.42
3.43-3.550.22411270.23162591X-RAY DIFFRACTION98.48
3.55-3.70.26741320.23352560X-RAY DIFFRACTION97.93
3.7-3.870.28471480.23452629X-RAY DIFFRACTION99.57
3.87-4.070.24051390.21792534X-RAY DIFFRACTION96.92
4.07-4.320.27421680.20732565X-RAY DIFFRACTION99.35
4.32-4.660.25091410.19122629X-RAY DIFFRACTION99.07
4.66-5.130.23171420.20122595X-RAY DIFFRACTION98.88
5.13-5.870.27861690.22842588X-RAY DIFFRACTION99.1
5.87-7.390.281330.2262651X-RAY DIFFRACTION98.97
7.39-78.330.1751260.1782671X-RAY DIFFRACTION98

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