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- PDB-3we4: Crystal structure of S6K1 kinase domain in complex with a pyrimid... -

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Basic information

Entry
Database: PDB / ID: 3we4
TitleCrystal structure of S6K1 kinase domain in complex with a pyrimidine derivative PF-4708671 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
ComponentsRibosomal protein S6 kinase beta-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE PROTEIN KINASE DOMAIN / TRANSFERASE / PHOSPHORYLATION / ATP-BINDING / ZINC-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


long-chain fatty acid import into cell / negative regulation of TORC2 signaling / cellular response to nutrient / TORC1 signaling / phosphatidylinositol-mediated signaling / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / cellular response to dexamethasone stimulus ...long-chain fatty acid import into cell / negative regulation of TORC2 signaling / cellular response to nutrient / TORC1 signaling / phosphatidylinositol-mediated signaling / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / cellular response to dexamethasone stimulus / behavioral fear response / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic cell cycle / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / modulation of chemical synaptic transmission / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / mitochondrial outer membrane / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / glutamatergic synapse / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5FI / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsNiwa, H. / Shirouzu, M. / Yokoyama, S.
CitationJournal: J.Struct.Funct.Genom. / Year: 2014
Title: Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Authors: Niwa, H. / Mikuni, J. / Sasaki, S. / Tomabechi, Y. / Honda, K. / Ikeda, M. / Ohsawa, N. / Wakiyama, M. / Handa, N. / Shirouzu, M. / Honma, T. / Tanaka, A. / Yokoyama, S.
History
DepositionJun 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6353
Polymers37,1791
Non-polymers4562
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.930, 70.930, 146.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Ribosomal protein S6 kinase beta-1 / S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / ...S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / Serine/threonine-protein kinase 14A / p70 ribosomal S6 kinase alpha


Mass: 37178.816 Da / Num. of mol.: 1 / Fragment: UNP residues 78-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23443, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5FI / 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole


Mass: 390.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21F3N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 3.7-3.9M sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 29, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.995→50 Å / Num. all: 26174 / Num. obs: 26174 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.12 / Net I/σ(I): 13.3
Reflection shellResolution: 1.995→2.03 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1292 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A62

3a62


Resolution: 1.995→35.465 Å / SU ML: 0.21 / σ(F): 1.08 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 2428 5.02 %RANDOM
Rwork0.1747 ---
obs0.1774 26102 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.86 Å2 / Biso mean: 51.0227 Å2 / Biso min: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 1.995→35.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 29 183 2498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072368
X-RAY DIFFRACTIONf_angle_d1.0113193
X-RAY DIFFRACTIONf_chiral_restr0.039343
X-RAY DIFFRACTIONf_plane_restr0.005401
X-RAY DIFFRACTIONf_dihedral_angle_d14.873907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9951-2.03580.31771500.29852661281197
2.0358-2.08010.30541320.271727542886100
2.0801-2.12850.26321210.251427292850100
2.1285-2.18170.25061620.226826922854100
2.1817-2.24070.25951330.216827372870100
2.2407-2.30660.22711460.207927092855100
2.3066-2.3810.25951610.204327112872100
2.381-2.46610.20051660.194926952861100
2.4661-2.56480.23421360.189327212857100
2.5648-2.68150.24821680.173527052873100
2.6815-2.82280.211380.181727422880100
2.8228-2.99960.22811680.180926892857100
2.9996-3.23110.27451410.177727452886100
3.2311-3.5560.26251280.165427332861100
3.556-4.06990.22911340.13882705283999
4.0699-5.12510.16321360.14062653278997
5.1251-35.47060.24031080.17512515262392
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.176-0.7222-1.05081.83870.71232.82350.0257-0.1944-0.13480.27980.0371-0.10770.15090.4427-0.06240.3318-0.00360.0060.4894-0.09520.3287-9.61768.3234-11.6328
22.8909-1.3947-1.47612.31681.0174.2935-0.09310.0949-0.30550.2387-0.07140.14940.0816-0.12440.02610.3095-0.0550.09890.3497-0.05840.3355-28.934114.3341-2.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 85:191 )A85 - 191
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 192:374 )A192 - 374

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