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- PDB-8fp1: PKCeta kinase domain in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 8fp1
TitlePKCeta kinase domain in complex with compound 2
ComponentsProtein kinase C eta type
KeywordsTRANSFERASE/INHIBITOR / HPK1 / Structure based drug design / cancer / kinase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / positive regulation of B cell receptor signaling pathway / protein kinase C signaling / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / positive regulation of macrophage derived foam cell differentiation / positive regulation of keratinocyte differentiation / regulation of bicellular tight junction assembly ...diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / positive regulation of B cell receptor signaling pathway / protein kinase C signaling / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / positive regulation of macrophage derived foam cell differentiation / positive regulation of keratinocyte differentiation / regulation of bicellular tight junction assembly / positive regulation of glial cell proliferation / positive regulation of protein localization to plasma membrane / small GTPase binding / G alpha (z) signalling events / cell-cell junction / positive regulation of NF-kappaB transcription factor activity / cell differentiation / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / enzyme binding / signal transduction / extracellular exosome / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein kinase C, eta / Novel protein kinase C eta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) ...Protein kinase C, eta / Novel protein kinase C eta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-XXF / Protein kinase C eta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJohnson, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design and Synthesis of Functionally Active 5-Amino-6-Aryl Pyrrolopyrimidine Inhibitors of Hematopoietic Progenitor Kinase 1.
Authors: Gallego, R.A. / Bernier, L. / Chen, H. / Cho-Schultz, S. / Chung, L. / Collins, M. / Del Bel, M. / Elleraas, J. / Costa Jones, C. / Cronin, C.N. / Edwards, M. / Fang, X. / Fisher, T. / He, M. ...Authors: Gallego, R.A. / Bernier, L. / Chen, H. / Cho-Schultz, S. / Chung, L. / Collins, M. / Del Bel, M. / Elleraas, J. / Costa Jones, C. / Cronin, C.N. / Edwards, M. / Fang, X. / Fisher, T. / He, M. / Hoffman, J. / Huo, R. / Jalaie, M. / Johnson, E. / Johnson, T.W. / Kania, R.S. / Kraus, M. / Lafontaine, J. / Le, P. / Liu, T. / Maestre, M. / Matthews, J. / McTigue, M. / Miller, N. / Mu, Q. / Qin, X. / Ren, S. / Richardson, P. / Rohner, A. / Sach, N. / Shao, L. / Smith, G. / Su, R. / Sun, B. / Timofeevski, S. / Tran, P. / Wang, S. / Wang, W. / Zhou, R. / Zhu, J. / Nair, S.K.
History
DepositionJan 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C eta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9862
Polymers40,5631
Non-polymers4231
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.340, 78.070, 93.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein kinase C eta type / PKC-L / nPKC-eta


Mass: 40563.035 Da / Num. of mol.: 1 / Fragment: residues 333-683 / Mutation: S675E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCH, PKCL, PRKCL / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24723, protein kinase C
#2: Chemical ChemComp-XXF / (3P)-3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undecan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile


Mass: 422.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.56 % / Description: Chunky 3D hexagonal rod
Crystal growTemperature: 286.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Well Ingredients: Precipitant: 21.0 %w/v (21.0 uL of stock 50.0 %w/v) PEG 3350 Salt: 0.7 M (4.375 uL of stock 8.0 M) lithium nitrate Buffer: 0.1 M (5.0 uL of stock 1.0 M) MES (pH 6.00) ...Details: Well Ingredients: Precipitant: 21.0 %w/v (21.0 uL of stock 50.0 %w/v) PEG 3350 Salt: 0.7 M (4.375 uL of stock 8.0 M) lithium nitrate Buffer: 0.1 M (5.0 uL of stock 1.0 M) MES (pH 6.00) Organic (non-volatile): 7.0 % w/v (4.375 uL of stock 80.0 % w/v) Glycerol

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Data collection

DiffractionMean temperature: 87.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.63 Å / Num. obs: 29645 / % possible obs: 82.1 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 1483 / CC1/2: 0.844

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Processing

Software
NameClassification
BUSTERrefinement
PHASERphasing
XDSdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1371 4.97 %RANDOM
Rwork0.1978 ---
obs0.1996 27573 82.8 %-
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.325 Å20 Å20 Å2
2---0.6745 Å20 Å2
3---0.3495 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.85→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 52 164 2859
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092772HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953754HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d970SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it2772HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion17.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
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_contact2334SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.87 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4132 -4.35 %
Rwork0.2332 528 -
all0.2406 552 -
obs--57.11 %

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