+Open data
-Basic information
Entry | Database: PDB / ID: 8pas | ||||||
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Title | Crystal structure of MAP4K1 with a SMOL inhibitor | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 1 | ||||||
Keywords | TRANSFERASE / kinase / inhibitor / drug discovery | ||||||
Function / homology | Function and homology information MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / protein autophosphorylation / cell population proliferation / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / protein autophosphorylation / cell population proliferation / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Friberg, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Identification and optimization of Azaindole based MAP4K1 Inhibitors and the discovery of BAY-405 Authors: Mowat, J. / Carretero, R. / Leder, G. / Aiguabella Font, N. / Neuhaus, R. / Berndt, S. / Guenther, J. / Friberg, A. / Schaefer, M. / Briem, H. / Raschke, M. / Miyatake Ondozabal, H. / ...Authors: Mowat, J. / Carretero, R. / Leder, G. / Aiguabella Font, N. / Neuhaus, R. / Berndt, S. / Guenther, J. / Friberg, A. / Schaefer, M. / Briem, H. / Raschke, M. / Miyatake Ondozabal, H. / Buchmann, B. / Boemer, U. / Hartung, I. / Offringa, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pas.cif.gz | 230.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pas.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pas_validation.pdf.gz | 849.6 KB | Display | wwPDB validaton report |
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Full document | 8pas_full_validation.pdf.gz | 862.7 KB | Display | |
Data in XML | 8pas_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 8pas_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/8pas ftp://data.pdbj.org/pub/pdb/validation_reports/pa/8pas | HTTPS FTP |
-Related structure data
Related structure data | 8parC 8pauC 8pavC 8pawC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32362.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q92918, non-specific serine/threonine protein kinase #2: Chemical | Mass: 570.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28F2N8O5 / Feature type: SUBJECT OF INVESTIGATION Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: NOT DISCLOSED |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→42.91 Å / Num. obs: 19051 / % possible obs: 96.1 % / Redundancy: 3 % / CC1/2: 0.999 / Rrim(I) all: 0.049 / Rsym value: 0.041 / Net I/σ(I): 21.55 |
Reflection shell | Resolution: 2.7→2.95 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4477 / CC1/2: 0.936 / Rrim(I) all: 0.529 / Rsym value: 0.439 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.91 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.895 / SU B: 45.126 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R: 1.494 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.876 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→42.91 Å
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