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- PDB-6h9b: 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazol... -

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Basic information

Entry
Database: PDB / ID: 6h9b
Title1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsTRANSPORT PROTEIN / cytoskeleton / cell division / intracellular transport
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FWH / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsVarela, P.F. / Gigant, B.
CitationJournal: J. Med. Chem. / Year: 2019
Title: 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin-Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation.
Authors: Naret, T. / Khelifi, I. / Provot, O. / Bignon, J. / Levaique, H. / Dubois, J. / Souce, M. / Kasselouri, A. / Deroussent, A. / Paci, A. / Varela, P.F. / Gigant, B. / Alami, M. / Hamze, A.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,03124
Polymers210,2965
Non-polymers3,73519
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21610 Å2
ΔGint-259 kcal/mol
Surface area67170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.940, 128.480, 251.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 48336.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0*PLUS
#2: Protein Tubulin beta chain


Mass: 48451.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16719.938 Da / Num. of mol.: 1 / Mutation: C14A, F20W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

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Non-polymers , 6 types, 249 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Mutation: C14A, F20W / Source method: isolated from a natural source / Formula: SO4 / Source: (natural) Rattus norvegicus (Norway rat)
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Mutation: C14A, F20W
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O14P3 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-FWH / 9-methyl-3-[1-(2-methylquinolin-4-yl)ethenyl]carbazole


Mass: 348.440 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C25H20N2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, LISO4, PIPES BUFFER, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.745→47.65 Å / Num. obs: 55767 / % possible obs: 99.58 % / Redundancy: 7.3 % / Biso Wilson estimate: 96 Å2 / Net I/σ(I): 10.41
Reflection shellResolution: 2.745→2.843 Å

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Processing

Software
NameClassification
XDSdata reduction
PHENIXphasing
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RYC

3ryc


Resolution: 2.75→47.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2789 5 %RANDOM
Rwork0.172 ---
obs0.174 55767 99.7 %-
Displacement parametersBiso mean: 108.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.8881 Å20 Å20 Å2
2--5.1089 Å20 Å2
3----1.2208 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.75→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14647 0 231 230 15108
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115234HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1320692HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5276SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2752HARMONIC5
X-RAY DIFFRACTIONt_it15234HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion19.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1961SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17435SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.77 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.361 -5.02 %
Rwork0.2794 1060 -
all0.2838 1116 -
obs--86.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9099-0.6876-0.32573.12551.12782.9253-0.11950.225-0.2975-0.0481-0.0448-0.02940.2370.17120.16430.752-0.01440.0298-0.4207-0.1168-0.436110.003832.662674.855
21.3501-1.57810.28424.10010.89571.39470.09250.3320.2653-0.3677-0.1182-0.4874-0.12920.26920.02570.73130.02050.0606-0.31030.0066-0.37682.51370.138591.6739
31.0576-1.18-0.30473.77481.46111.49690.03860.07320.1443-0.4582-0.076-0.4821-0.14710.05010.03740.74380.07750.0392-0.378-0.0141-0.2991-12.5903109.16103.262
42.3334-1.2637-0.8353.06440.79832.67170.31460.34810.133-0.3533-0.3098-0.1622-0.26370.1573-0.00480.32530.0483-0.0142-0.5676-0.0352-0.5549-32.9793143.28116.834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|604 E|4 - E|64 }
2X-RAY DIFFRACTION2{ B|1 - B|701 E|65 - E|89 }
3X-RAY DIFFRACTION3{ C|1 - C|604 E|90 - E|115 }
4X-RAY DIFFRACTION4{ D|1 - D|701 E|116 - E|147 }

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