Primary Citation PubMed: 15014504
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The roles of beta-tubulin mutations and isotype expression in acquired drug resistance.
(2007) Cancer Inform 3
PubMed: 19455242 | PubMedCentral: PMC2675838 | DOI: null
Structures of the paclitaxel (PTX), colchicine (CN) and vinblastine (VLB) from structural files 1JFF, 1SA0 and 1Z2B have been superimposed and fit back onto the 1SA0 structure to obtain the relative p... sitioning of each drug within the protofilament.
Two higher resolution structures, 1SA0 and 1SA1 followed, producing structures of the colchicine and podophyllotoxin bound complexes ( Ravelli et al. 2004 ), while both the colchicine and vinblastine binding sites are observed in 1Z2B ( Gigant et al. 2005 ).
The columns representing drug interactions indicate residues in which any atom is within 6 Å of any atom within the bound drug molecule from structural files 1JFF, 1SA0 and 1Z2B for Paclitaxel (PTX), Colchicine (CN) and Vinblastine (VLB) respectively.
Publication Year: 2007
A new model for binding of kinesin 13 to curved microtubule protofilaments.
(2009) J Cell Biol 185
PubMed: 19332892 | PubMedCentral: PMC2700504 | DOI: 10.1083/jcb.200812052
(C) Model of the crystal structures of truncated NM (Protein Data Bank reference codes 2HEH and 1v8k) fitted onto straight (Protein Data Bank reference code 1tub) and bent tubulin (Protein Data Bank r... ference code 1sa0).
Publication Year: 2009
Motor domain phosphorylation and regulation of the Drosophila kinesin 13, KLP10A.
(2009) J Cell Biol 186
PubMed: 19687256 | PubMedCentral: PMC2733746 | DOI: 10.1083/jcb.200902113
1SA0 ; α-tubulin, 37–46 and 279–284; β-tubulin, 276–283) were constructed from idealized internal coordinates.
Quantitative analysis of the effect of tubulin isotype expression on sensitivity of cancer cell lines to a set of novel colchicine derivatives.
(2010) Mol Cancer 9
PubMed: 20509970 | PubMedCentral: PMC2890610 | DOI: 10.1186/1476-4598-9-131
Recently, this work was followed by an additional structure that identified colchicine as binding between the α and β tubulin molecules of the hetero-dimer itself (PDB identifier 1SA0)...
Publication Year: 2010
Cancer cells acquire mitotic drug resistance properties through beta I-tubulin mutations and alterations in the expression of beta-tubulin isotypes.
(2010) PLoS One 5
PubMed: 20838440 | PubMedCentral: PMC2933234 | DOI: 10.1371/journal.pone.0012564
The three-dimensional tubulin structure (PDB code: 1SA0) was used  and the program Discovery Studio 2.1 (Accelrys, Inc) was applied to build model by mutating residues and performi... g energy minimization.
The three-dimensional structure of wild-type tubulin (PDB code: 1SA0) was used as a template to perform energy minimization.
Applying an empirical hydropathic forcefield in refinement may improve low-resolution protein X-ray crystal structures.
(2011) PLoS One 6
PubMed: 21246043 | PubMedCentral: PMC3016398 | DOI: 10.1371/journal.pone.0015920
g009 Figure 9 Superposition of Cα atoms in structural models for αβ-tubulin (1SA0): PDB deposited model (black), refined with native CNS (red) and CNS+HINT (blue), comp... exed with colchicine (spacefill, colored by atom).
Refinement of “authentic” low-resolution datasets As a final test, we have re-refined three datasets with resolutions between 3.5 and 4.0 Å: 3GEC  (4.00 Å), 1ISR  (4.00 Å) and 1SA0  (3.58 Å).
CNS protocol measure PDB deposited native v. 1.1 w/HINT † 3GEC (4.00 Å) *  R 0.244 * 0.267 0.279 R free 0.312 * 0.347 0.339 E HINT (kcal mol −1 ) 171.1 ‡ −6.0 −69.6 Ramachandran score 65.5 68.3 77.5 clashscore 58.42 63.80 23.77 1ISR (4.00 Å) *  R 0.237 * 0.199 0.203 R free 0.259 * 0.270 0.274 E HINT (kcal mol −1 ) 2.3 ‡ −51.1 −138.5 Ramachandran score 84.8 81.8 88.1 clashscore 104.51 73.33 72.65 1SA0 (3.58 Å) *  R 0.232 * 0.267 0.264 R free 0.249 * 0.335 0.328 E HINT (kcal mol −1 ) 129.8 ‡ −161.0 −377.2 Ramachandran score 79.8 83.6 85.1 clashscore 18.33 2.35 1.12 *Values reported in PDB file headers.
Publication Year: 2011
In silico study of fucoxanthin as a tumor cytotoxic agent.
(2012) J Pharm Bioallied Sci 4
PubMed: 22368399 | PubMedCentral: PMC3283957 | DOI: 10.4103/0975-7406.92733
The pdb files were 1JFF[ 20 ] (with paclitaxel ligand), 1SA0[ 21 ] (with colchicine ligand) and 1Z2B[ 22 ] (with vinblastine ligand).
Docking of fucoxanthin to subjected receptors were -6.2 (1RV1), -9.3 (1AQ1), -8.1 (1JFF), -9.2 (1SA0), and -7.2 (1Z2B) kcal/mol.
Publication Year: 2012
Rationalization of paclitaxel insensitivity of yeast ?-tubulin and human ?III-tubulin isotype using principal component analysis.
(2012) BMC Res Notes 5
PubMed: 22849332 | PubMedCentral: PMC3477043 | DOI: 10.1186/1756-0500-5-395
The structures for paclitaxel-bound (PDB ID: 1JFF) [ 23 ] and paclitaxel-free (PDB ID: 1SA0) [ 34 ] tubulin were downloaded from the protein data bank [ 35 ].
As shown in Figure 4 d, Lys19, Phe20, Val23, and Asp26 β-tubulin is part of a helix in paclitaxel-bound (pdb code: 1JFF) as well as in paclitaxel-free (pdb code: 1SA0) structure.
That the loops are flexible and become more ordered upon binding paclitaxel is clear from the fact that in the paclitaxel-free state (pdb ID:1SA0), residues 278 to 285 in one of the loops is disordered in β-tubulin.
Figure 4 Paclitaxel-bound (pdb ID:1JFF) and paclitaxel-free (pdb ID: 1SA0) β-tubulin.
In the paclitaxel-bound state, the side chain hydroxyl group of Ser280 forms a H-bond with the side chain nitrogen of Lys218 (note that residue 280 is disordered in 1SA0 and so no such interaction is present).
d) An α-helix in β-tubulin (containing residues 19, 20 and 23) as found in two crystal structures: 1SA0 (paclitaxel-free) and 1JFF (paclitaxel-bound).
Novel indole-bearing combretastatin analogues as tubulin polymerization inhibitors.
(2013) Org Med Chem Lett 3
PubMed: 23452433 | PubMedCentral: PMC3599526 | DOI: 10.1186/2191-2858-3-3
Material and methods for molecular docking The coordinates of tubulin were obtained from protein data bank [PDB:1SA0] [ 19 , 20 ].
To validate the docking procedure for the prediction of the correct binding mode of inhibitor at the colchicine-binding site, the colchicine was extracted from the original X-ray structure [PDB:1SA0] [ 19 , 20 ] and re-docked using GOLD.21.
Publication Year: 2013
Determination of the optimal tubulin isotype target as a method for the development of individualized cancer chemotherapy.
(2013) Theor Biol Med Model 10
PubMed: 23634782 | PubMedCentral: PMC3651705 | DOI: 10.1186/1742-4682-10-29
The paclitaxel complex is based on PDB:1JFF, the colchicine complex is based on PDB:1SA0, and the vinblastine complex is based on PDB:1Z2B.
NMK-TD-100, a novel microtubule modulating agent, blocks mitosis and induces apoptosis in HeLa cells by binding to tubulin.
(2013) PLoS One 8
PubMed: 24116100 | PubMedCentral: PMC3792137 | DOI: 10.1371/journal.pone.0076286
To predict whether colchicine interferes with the binding of NMK-TD-100, the crystal structure of αβ -tubulin (PDB ID: 1SA0) was utilized as template for this docking study [ 42 ].
pdb file) in 1SA0.
Rational design, synthesis, and biological evaluation of third generation ?-noscapine analogues as potent tubulin binding anti-cancer agents.
PubMed: 24205049 | PubMedCentral: PMC3804772 | DOI: 10.1371/journal.pone.0077970
Protein preparation The co-crystallized colchicine-tubulin complex structure (PDB ID: 1SA0, resolution 3.58Å) [ 38 ] was used for molecular docking and rescoring.
The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.
(2014) PLoS Comput Biol 10
PubMed: 24516374 | PubMedCentral: PMC3916224 | DOI: 10.1371/journal.pcbi.1003464
g001 Figure 1 Conformational rearrangements of α- and β-subunits of the straight (PDB entry 1JFF  , resolution 3.5 Å) and bent (PDB entry 1SA0  , resolution 3.58 Å... ) tubulin heterodimers.
Methods Preparation of endpoint structures of conformational landscapes Selection of straight and bent tubulin endpoint structures Conformational change coordinates for tubulin are bounded by the taxol-liganded straight tubulin heterodimer, observed in zinc-induced protofilament sheets (PDB id 1JFF, resolution 3.5 Å, organism B. taurus ), and the bent tubulin structure observed in the α 1 β 1 heterodimer of the T2R-colchicine complex (PDB id 1SA0, resolution 3.58 Å, organism B. taurus ) (see Figure S1 in Text S1 ).
Soluble GDP-tubulin was previously thought to exist in only two states, the “straight” and “bent” structures represented by PDB ids 1JFF and 1SA0, respectively.
The 1SA0 α 1 β 1 heterodimer from the T2R-colchicine:tubulin complex exhibits a ∼8.3° twist angle, which is somewhat large compared to the degree of twisting exhibited by the newer X-ray crystallographic structures of tubulins, whose twist angles range from ∼5–7° (see Tables S2a–b in Text S1 ).
Publication Year: 2014
Docking, synthesis and antiproliferative activity of N-acylhydrazone derivatives designed as combretastatin A4 analogues.
(2014) PLoS One 9
PubMed: 24614859 | PubMedCentral: PMC3948622 | DOI: 10.1371/journal.pone.0085380
Figure S4 Compounds 5i (A), 5k (B), 5n (C) and 11 (D) poses at colchicine binding site of β-tubulin protein (PDB:1sa0).
g002 Figure 2 Initial conception and molecular design of N -acylhydrazone derivatives 5a–s. Results and Discussion All designed compounds were predicted to favorably interact with the DAMA-colchicine binding site in β-tubulin (PDB code: 1sa0)  .
g003 Figure 3 Polar interactions between CA-4 (A) or LASSBio-1593 (B) with the colchicine binding site of β-tubulin (PDB code: 1sa0).
The fitness function was selected after redocking experiments with colchicine in the binding site of β-tubulin (PDB code: 1sa0).
g008 Figure 8 Best poses of compounds 5b (A), 10 (B), 9 (C) and 12 (D) at the colchicine binding pocket β-tubulin (PDB code: 1sa0).
Figure S2 The pose of CA-4 Z-isomer (A) and E-isomer (B) at colchicine binding site of β-tubulin protein (PDB:1sa0).
The most stable conformer of each structure was reoptimized with the AM1 semiempirical molecular orbital method  and saved as mol2 files for docking studies into the colchicine binding site of the β-tubulin crystallographic structure available in the Protein Data Bank with code 1sa0.
Optimization of 4-(N-cycloamino)phenylquinazolines as a novel class of tubulin-polymerization inhibitors targeting the colchicine site.
(2014) J Med Chem 57
PubMed: 24502232 | PubMedCentral: PMC3983391 | DOI: 10.1021/jm4016526
Figure 5 Predicted binding mode of 5f (orange stick) with tubulin (PDB code: 1SA0) and overlapping with DAMA-colchicine (cyan, the bound ligand of 1SA0).
The crystal structure of tubulin in complex with DAMA-colchicine (PDB code: 1SA0) was downloaded from the RCSB Protein Data Bank ( http://www.rcsb.org/pdb ) for use in the modeling study.
Molecular Modeling To elucidate the binding characteristics of these new compounds with tubulin, we performed docking studies with the most active compound, 5f , at the colchicine binding pocket using the CDOCKER program in the Discovery Studio 3.0 software and the tubulin crystal structure (PDB code: 1SA0) 27 , 28 in comparison with the original ligand, N -deacetyl- N -(2-mercaptoacetyl)-colchicine (DAMA-colchicine, Figure 1 ).
PubMed ID is not available.
Published in 2014
The initial coordinates for tubulin was taken from the crystal structure of tubulin in complex with colchicine (PDB: 1SA0.
A novel sulfonamide agent, MPSP-001, exhibits potent activity against human cancer cells in vitro through disruption of microtubule.
(2012) Acta Pharmacol Sin 33
PubMed: 22301862 | PubMedCentral: PMC4010333 | DOI: 10.1038/aps.2011.156
Molecular modeling The X-ray crystal structure of α,β-tubulin complexed with N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) was obtained from the Brookhaven Protein Data ... ank (entry code: 1SA0 29 ) as the target structures in the molecular docking.
Tubulin inhibitors: pharmacophore modeling, virtual screening and molecular docking.
(2014) Acta Pharmacol Sin 35
PubMed: 24909516 | PubMedCentral: PMC4088285 | DOI: 10.1038/aps.2014.34
A crystal structure of tubulin, which was obtained at 3.58 Å, was downloaded from the protein data bank (PDB ID: 1SA0).
Molecular docking To further refine the retrieved hits and remove the false positives, these 952 compounds, as well as the 26 training-set compounds, were docked into the colchicine-binding site of tubulin (PDB ID: 1SA0) using the Molecular Operating Environment (MOE) software.
The crystal structure of tubulin with colchicine was obtained from the protein data bank (PDB ID: 1SA0).
A tethered delivery mechanism explains the catalytic action of a microtubule polymerase.
(2014) Elife 3
PubMed: 25097237 | PubMedCentral: PMC4145800 | DOI: 10.7554/eLife.03069
Ravelli RB , Gigant B , Curmi PA , Jourdain I , Lachkar S , Sobel A , Knossow M , 2004 , Tubulin-colchicine: stathmin-like domain complextubulin-colchicine: stathmin-like domain complex , http://www.p... b.org/pdb/explore/explore.do?structureId=1SA0 , Publicly available at RCSB Protein Data Bank.
To calculate sedimentation coefficients, we first prepared compact ‘longitudinal’ and ‘lateral’ models by docking the TOG1 and TOG2 complexes onto the αβ-tubulins in the stathmin complex (pdb 1SA0 [ Ravelli et al., 2004 ]) and a section of microtubule (coordinates provided by Ken Downing, Lawrence Berkeley lab), respectively.
When 4 and 7 were docked into the colchicine binding site in tubulin (Figure 4 , PDB code 1SA0), they showed very similar binding poses and overlapped with the native ligand reasonably well.
Figure 4 Potential binding poses for 4 (gold tube model; glide docking score −8.58) and 7 (dark green tube model; glide docking score −8.10) in tubulin α,β-dimer (PDB code 1SA0).
C Ring Modification: H-Bonding and Alkylation of the Colchicine Binding Site The methoxy groups in the TMP ring were known to interact with Cys-241 residue of DAMA–colchicine in the cocrystallized tubulin structure (PDB code 1SA0).
Figure 5 Potential binding poses for 33 (gray tube model; glide docking score of −8.70) and the native ligand DAMA–colchicine (blue thin wire model; glide docking score of −9.26) in tubulin α,β-dimer (PDB Code: 1SA0).
(C 23 H 19 N 3 O 4 S) C, H, N. Molecular Modeling The molecular modeling studies were performed with the published crystal structures of the α,β-tubulin dimer in complex with DAMA–colchicine (Protein Data Bank code 1SA0).
Target Based Designing of Anthracenone Derivatives as Tubulin Polymerization Inhibiting Agents: 3D QSAR and Docking Approach.
(2014) Int J Med Chem 2014
PubMed: 25383219 | PubMedCentral: PMC4207406 | DOI: 10.1155/2014/658016
Crystal structures of tubulin protein in complex with colchicine (PDB ID: 1SA0) [ 35 ] with resolution 3.5 Å was downloaded from RCSB Protein Data Bank to serve as the docking template...
Our most active, selected representative compounds (16c, 16f, 16h, 20c, 20i, and 31a–e) were modeled by positioning them in the colchicine (PDB ID: 1SA0) binding site in accordance with the published crystal structure of colchicine bound in the domain of chains A and B.
Suprafenacine, an indazole-hydrazide agent, targets cancer cells through microtubule destabilization.
PubMed: 25354194 | PubMedCentral: PMC4212991 | DOI: 10.1371/journal.pone.0110955
The compounds (colchicine or SRF) were docked into the colchicine-binding pocket of tubulin using the crystal structure of the tubulin-colchicine: stathmin-like domain [PDB code: 1SA0].
Using the crystal structure of the tubulin-colchicine: stathmin-like domain (PDB 1SA0), both colchicine [ Figure 2C ] and SRF [ Figure 2D ] were docked into the colchicine-binding pocket of tubulin.
1SA0 ] are shown in yellow and orange).
Design, Synthesis and Cytotoxicity Evaluationof New 1,2-diaryl-4, 5, 6, 7-Tetrahydro-1H-benzo[d] Imidazolesas Tubulin Inhibitors.
(2015) Iran J Pharm Res 14
PubMed: 25561912 | PubMedCentral: PMC4277619 | DOI: null
The tubulin structure was downloaded from the PDB data bank (http://www.rcsb.org/ - PDB code: 1SA0) ( 31 , 32 ).
Crystallized ligand was removed from crystal protein (1SA0).
Publication Year: 2015
In-silico Investigation of Tubulin Binding Modes of a Series of Novel Antiproliferative Spiroisoxazoline Compounds Using Docking Studies.
PubMed: 25561920 | PubMedCentral: PMC4277627 | DOI: null
The crystal structure of tubulin (PDB code: 1SA0) was obtained from the Protein Data Bank at RCSB (http://www.rcsb.org).
Tubulin experimental structure (PDB code 1SA0) was used for the docking calculation and the essential amino acid residues at the binding site are indicated.
Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the ?-? interfacial site of human tubulin.
(2014) BMC Genomics 15 Suppl 9
PubMed: 25521775 | PubMedCentral: PMC4290613 | DOI: 10.1186/1471-2164-15-S9-S3
The homology model was obtained using Modeller 9.11 [ 43 - 46 ] taking Bos taurus tubulin B-chain [PDB ID: 1SA0] as the template [ 12 ].
Published in 2015
Structural alignment of compounds 6–12 within the colchicine-binding pocket of the colchicine-tubulin crystal structure (PDB: 1SA0) using the MOE FlexAlign protocol followed by an energy minim... zation procedure to simulate the “induced-fit” effect.
To test this hypothesis, we performed a structural alignment of compound 6 with colchicine and docked the aligned conformations onto the ligand-bound tubulin crystal structure (PDB: 1SA0) ( Fig. 5C ).
Molecular modeling The crystal structure of colchicine-bound tubulin was downloaded from the PDB database (PDB code: 1SA0) and the beta tubulin monomer with bound colchicine (chain D) was extracted from the protein model [ 69 ].
Compounds 7k and 1 were docked into the colchicine binding site of tubulin (PDB ID: 1SA0).
The structures were docked into the colchicine binding site of tubulin (PDB ID: 1SA0).
Docking study The initial coordinates for tubulin were taken from the crystal structure of tubulin in complex with colchicine (PDB ID: 1SA0) obtained from the Protein Data Bank.
The X-ray crystal structure of the DAMA-colchicine-tubulin complex (PDB entry: 1SA0) was used as the tubulin protein template.
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