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- PDB-4yht: bRaf complexed with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 4yht
TitlebRaf complexed with an inhibitor
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTransferase/Transferase Inhibitor / kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


Signalling to p38 via RIT and RIN / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / MAP kinase kinase activity / positive regulation of peptidyl-serine phosphorylation ...Signalling to p38 via RIT and RIN / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / MAP kinase kinase activity / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / postsynaptic modulation of chemical synaptic transmission / animal organ morphogenesis / cellular response to calcium ion / RAF activation / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Negative regulation of MAPK pathway / Signaling by BRAF and RAF1 fusions / cell body / scaffold protein binding / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynapse / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / calcium ion binding / negative regulation of apoptotic process / glutamatergic synapse / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / 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 / C1-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / 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. / 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-4EF / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.05 Å
AuthorsShewchuk, L.M. / Lawhorn, B.G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: GSK114: A selective inhibitor for elucidating the biological role of TNNI3K.
Authors: Lawhorn, B.G. / Philp, J. / Graves, A.P. / Shewchuk, L. / Holt, D.A. / Gatto, G.J. / Kallander, L.S.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase B-raf
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9876
Polymers61,9572
Non-polymers1,0304
Water1,29772
1
A: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4943
Polymers30,9791
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4943
Polymers30,9791
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.783, 99.783, 161.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A448 - 626
2112B448 - 626
1122A626 - 630
2122B626 - 630
1132A631 - 661
2132B631 - 661
1142A663 - 719
2142B663 - 719
1151A2001
2151B2001

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.078417, -0.994866, -0.063966), (-0.994774, 0.073879, 0.070467), (-0.065379, 0.069157, -0.995461)-57.776951, -48.836781, -71.072197

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Components

#1: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 30978.697 Da / Num. of mol.: 2 / Fragment: UNP residues 449-720 / Mutation: I542T, I543N, I550T, L705T, L715T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: unidentified baculovirus
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-4EF / 3-[(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-N-methyl-4-(morpholin-4-yl)benzenesulfonamide


Mass: 422.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19ClN6O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris pH 8.0, 650 mM NaCl, 3-6 % PEG 8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 16082 / % possible obs: 99.3 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.153 / Χ2: 1.401 / Net I/av σ(I): 16 / Net I/σ(I): 6.1 / Num. measured all: 139786
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.18.70.6927981.29199.9
3.1-3.168.90.67811.41100
3.16-3.228.70.5638001.396100
3.22-3.2990.4837761.427100
3.29-3.368.90.3948011.33299.8
3.36-3.438.80.3217921.323100
3.43-3.5290.2937871.40999.9
3.52-3.628.80.2377881.33299.9
3.62-3.728.80.1997941.41499.7
3.72-3.848.80.1797951.34599.6
3.84-3.988.80.1477941.32199.9
3.98-4.148.80.128011.30999.6
4.14-4.338.80.1028001.31299.6
4.33-4.568.70.18071.40499
4.56-4.848.70.0988011.47499.3
4.84-5.218.60.1088071.70399.1
5.21-5.748.60.1298071.78898.7
5.74-6.578.40.1128301.59198.5
6.57-8.278.10.068331.27197.5
8.27-5080.0388901.18196.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.05→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 30.849 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 806 5 %RANDOM
Rwork0.1986 ---
obs0.2003 15207 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.35 Å2 / Biso mean: 48.996 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 68 72 4192
Biso mean--38.41 29.37 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194210
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9675693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06424.033181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51115727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3231523
X-RAY DIFFRACTIONr_chiral_restr0.080.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213173
X-RAY DIFFRACTIONr_mcbond_it1.6162.4142050
X-RAY DIFFRACTIONr_mcangle_it2.8143.6042552
X-RAY DIFFRACTIONr_scbond_it1.7332.4582160
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1638MEDIUM POSITIONAL0.030.5
1664TIGHT THERMAL3.510.5
1638MEDIUM THERMAL4.082
213MEDIUM POSITIONAL0.030.5
212TIGHT THERMAL1.950.5
213MEDIUM THERMAL1.322
3130MEDIUM POSITIONAL0.040.5
3124TIGHT THERMAL1.410.5
3130MEDIUM THERMAL2.092
4210MEDIUM POSITIONAL0.040.5
4224TIGHT THERMAL1.790.5
4210MEDIUM THERMAL2.92
528TIGHT THERMAL3.290.5
LS refinement shellResolution: 3.05→3.131 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 63 -
Rwork0.252 1105 -
all-1168 -
obs--98.65 %
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)
11.25851.21050.75332.41521.62062.2727-0.12580.17420.021-0.07430.1412-0.1669-0.09220.0287-0.01540.2449-0.0225-0.01720.3368-0.04680.0456-9.423-22.849-28.297
21.77090.74661.49120.76530.27852.0023-0.03940.0189-0.0892-0.04390.1175-0.0121-0.06440.0418-0.0780.2994-0.032-0.00050.3363-0.05930.0229-32.473-43.187-44.04
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A448 - 2001
2X-RAY DIFFRACTION2B448 - 2001

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