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Open data
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Basic information
Entry | Database: PDB / ID: 7r9l | ||||||
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Title | Crystal structure of HPK1 in complex with compound 2 | ||||||
![]() | Hematopoietic progenitor kinase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / inhibitor / MAP4K1 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, P. / Lehoux, I. / Wang, W. | ||||||
![]() | ![]() Title: Discovery of Spiro-azaindoline Inhibitors of Hematopoietic Progenitor Kinase 1 (HPK1). Authors: Chan, B.K. / Seward, E. / Lainchbury, M. / Brewer, T.F. / An, L. / Blench, T. / Cartwright, M.W. / Chan, G.K.Y. / Choo, E.F. / Drummond, J. / Elliott, R.L. / Gancia, E. / Gazzard, L. / Hu, B. ...Authors: Chan, B.K. / Seward, E. / Lainchbury, M. / Brewer, T.F. / An, L. / Blench, T. / Cartwright, M.W. / Chan, G.K.Y. / Choo, E.F. / Drummond, J. / Elliott, R.L. / Gancia, E. / Gazzard, L. / Hu, B. / Jones, G.E. / Luo, X. / Madin, A. / Malhotra, S. / Moffat, J.G. / Pang, J. / Salphati, L. / Sneeringer, C.J. / Stivala, C.E. / Wei, B. / Wang, W. / Wu, P. / Heffron, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r9nC ![]() 7r9pC ![]() 7r9tC ![]() 6cqeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33120.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92918, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-2YE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.47 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl, pH 8.5, 0.25 M sodium tartrate and 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→66.257 Å / Num. obs: 8574 / % possible obs: 92 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.42 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.054 / Rrim(I) all: 0.12 / Net I/σ(I): 8.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CQE Resolution: 2.332→66.257 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.19 Å2 / Biso mean: 62.2799 Å2 / Biso min: 18.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.332→66.257 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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