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- PDB-5oct: Discovery of small molecules binding to KRAS via high affinity an... -

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Basic information

Entry
Database: PDB / ID: 5oct
TitleDiscovery of small molecules binding to KRAS via high affinity antibody fragment competition method.
ComponentsGTPase KRas
KeywordsHYDROLASE / Domain antibodies / small molecules / drug fragment screening
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Signaling by SCF-KIT / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9R5 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / DI(HYDROXYETHYL)ETHER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsCruz-Migoni, A. / Ehebauer, M.T. / Phillips, S.E.V. / Quevedo, C.E. / Rabbitts, T.H.
CitationJournal: Nat Commun / Year: 2018
Title: Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment.
Authors: Quevedo, C.E. / Cruz-Migoni, A. / Bery, N. / Miller, A. / Tanaka, T. / Petch, D. / Bataille, C.J.R. / Lee, L.Y.W. / Fallon, P.S. / Tulmin, H. / Ehebauer, M.T. / Fernandez-Fuentes, N. / ...Authors: Quevedo, C.E. / Cruz-Migoni, A. / Bery, N. / Miller, A. / Tanaka, T. / Petch, D. / Bataille, C.J.R. / Lee, L.Y.W. / Fallon, P.S. / Tulmin, H. / Ehebauer, M.T. / Fernandez-Fuentes, N. / Russell, A.J. / Carr, S.B. / Phillips, S.E.V. / Rabbitts, T.H.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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_conn_type / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
C: GTPase KRas
D: GTPase KRas
E: GTPase KRas
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,24929
Polymers128,9896
Non-polymers5,26023
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint-90 kcal/mol
Surface area40020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.490, 118.450, 155.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA-3 - 16815 - 186
21GLUGLUBB-3 - 16815 - 186
12GLUGLUAA-3 - 16815 - 186
22GLUGLUCC-3 - 16815 - 186
13LYSLYSAA-3 - 16715 - 185
23LYSLYSDD-3 - 16715 - 185
14GLUGLUAA-3 - 16815 - 186
24GLUGLUEE-3 - 16815 - 186
15GLUGLUAA-3 - 16815 - 186
25GLUGLUFF-3 - 16815 - 186
16GLUGLUBB-3 - 16815 - 186
26GLUGLUCC-3 - 16815 - 186
17LYSLYSBB-3 - 16715 - 185
27LYSLYSDD-3 - 16715 - 185
18GLUGLUBB-3 - 16815 - 186
28GLUGLUEE-3 - 16815 - 186
19GLUGLUBB-3 - 16815 - 186
29GLUGLUFF-3 - 16815 - 186
110HISHISCC-3 - 16615 - 184
210HISHISDD-3 - 16615 - 184
111GLUGLUCC-3 - 16815 - 186
211GLUGLUEE-3 - 16815 - 186
112GLUGLUCC-3 - 16815 - 186
212GLUGLUFF-3 - 16815 - 186
113HISHISDD-3 - 16615 - 184
213HISHISEE-3 - 16615 - 184
114HISHISDD-3 - 16615 - 184
214HISHISFF-3 - 16615 - 184
115GLUGLUEE-3 - 16815 - 186
215GLUGLUFF-3 - 16815 - 186

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21498.164 Da / Num. of mol.: 6 / Mutation: Q61H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116

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Non-polymers , 6 types, 393 molecules

#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-9R5 / [(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine


Mass: 199.634 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C9H10ClNO2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8-15% w/v PEG 3350 and 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→41.72 Å / Num. obs: 72162 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.067 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFT

3gft


Resolution: 2.07→41.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.335 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21843 3573 5 %RANDOM
Rwork0.18787 ---
obs0.18936 68511 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.632 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--1.99 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.07→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 326 370 8680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198459
X-RAY DIFFRACTIONr_bond_other_d0.0030.027682
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.98511450
X-RAY DIFFRACTIONr_angle_other_deg1.031317796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.60224.24408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.777151454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371559
X-RAY DIFFRACTIONr_chiral_restr0.1010.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029526
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021729
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.863.8433991
X-RAY DIFFRACTIONr_mcbond_other3.8593.8423990
X-RAY DIFFRACTIONr_mcangle_it5.525.7354970
X-RAY DIFFRACTIONr_mcangle_other5.525.7364971
X-RAY DIFFRACTIONr_scbond_it5.7044.7764468
X-RAY DIFFRACTIONr_scbond_other5.7044.7764469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6956.8746480
X-RAY DIFFRACTIONr_long_range_B_refined10.93147.2979513
X-RAY DIFFRACTIONr_long_range_B_other10.93147.2989514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108280.08
12B108280.08
21A106100.08
22C106100.08
31A106700.07
32D106700.07
41A105820.07
42E105820.07
51A107500.07
52F107500.07
61B106700.07
62C106700.07
71B106900.06
72D106900.06
81B106060.06
82E106060.06
91B107180.07
92F107180.07
101C106620.06
102D106620.06
111C106580.07
112E106580.07
121C106760.07
122F106760.07
131D106160.06
132E106160.06
141D106940.06
142F106940.06
151E107260.07
152F107260.07
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 262 -
Rwork0.294 4983 -
obs--99.96 %

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