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- PDB-4c4g: Structure-based design of orally bioavailable pyrrolopyridine inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c4g | ||||||
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Title | Structure-based design of orally bioavailable pyrrolopyridine inhibitors of the mitotic kinase MPS1 | ||||||
![]() | DUAL SPECIFICITY PROTEIN KINASE TTK | ||||||
![]() | TRANSFERASE / PROTEIN KINASE / MITOSIS / STRUCTURE-BASED DESIGN | ||||||
Function / homology | ![]() protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naud, S. / Westwood, I.M. / Faisal, A. / Sheldrake, P. / Bavetsias, V. / Atrash, B. / Liu, M. / Hayes, A. / Schmitt, J. / Wood, A. ...Naud, S. / Westwood, I.M. / Faisal, A. / Sheldrake, P. / Bavetsias, V. / Atrash, B. / Liu, M. / Hayes, A. / Schmitt, J. / Wood, A. / Choi, V. / Boxall, K. / Mak, G. / Gurden, M. / Valenti, M. / de Haven Brandon, A. / Henley, A. / Baker, R. / McAndrew, C. / Matijssen, B. / Burke, R. / Eccles, S.A. / Raynaud, F.I. / Linardopoulos, S. / van Montfort, R. / Blagg, J. | ||||||
![]() | ![]() Title: Structure-Based Design of Orally Bioavailable 1H-Pyrrolo[3, 2-C]Pyridine Inhibitors of the Mitotic Kinase Monopolar Spindle 1 (Mps1). Authors: Naud, S. / Westwood, I.M. / Faisal, A. / Sheldrake, P.W. / Bavetsias, V. / Atrash, B. / Cheung, K.J. / Liu, M. / Hayes, A. / Schmitt, J. / Wood, A. / Choi, V. / Boxall, K. / Mak, G. / ...Authors: Naud, S. / Westwood, I.M. / Faisal, A. / Sheldrake, P.W. / Bavetsias, V. / Atrash, B. / Cheung, K.J. / Liu, M. / Hayes, A. / Schmitt, J. / Wood, A. / Choi, V. / Boxall, K. / Mak, G. / Gurden, M. / Valenti, M. / De-Haven-Brandon, A. / Henley, A. / Baker, R. / Mcandrew, C. / Matijssen, B. / Burke, R. / Hoelder, S. / Eccles, S.A. / Raynaud, F.I. / Linardopoulos, S. / Van Montfort, R.L.M. / Blagg, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.3 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 892.2 KB | Display | ![]() |
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Full document | ![]() | 894.4 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c4eC ![]() 4c4fC ![]() 4c4hC ![]() 4c4iC ![]() 4c4jC ![]() 4bi1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36195.234 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 519-808 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-7RO / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE INCLUDING HEXAHISTID | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 30-35% AQUEOUS PEG300 ONLY, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→41.04 Å / Num. obs: 13230 / % possible obs: 99.1 % / Observed criterion σ(I): 1.5 / Redundancy: 4.6 % / Biso Wilson estimate: 99.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.6 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BI1 Resolution: 2.65→41.04 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE LIGAND USED FOR SOAKING WAS 3- CHLORO-N,N-DIMETHYL-4-(2- (1-METHYL-1H-PYRAZOL-4-YL)-1H- PYRROLO(3,2-C)PYRIDIN-6- YLAMINO)BENZAMIDE BUT THE N-BOC PRECURSOR MODELLED HEREIN WAS DETECTED AS ...Details: THE LIGAND USED FOR SOAKING WAS 3- CHLORO-N,N-DIMETHYL-4-(2- (1-METHYL-1H-PYRAZOL-4-YL)-1H- PYRROLO(3,2-C)PYRIDIN-6- YLAMINO)BENZAMIDE BUT THE N-BOC PRECURSOR MODELLED HEREIN WAS DETECTED AS AN IMPURITY AT LESS THAN 2 PERCENT BY LCMS.
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Displacement parameters | Biso mean: 103.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.514 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→41.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.86 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 4.9899 Å / Origin y: 32.4446 Å / Origin z: 129.678 Å
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Refinement TLS group | Selection details: CHAIN A |