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- PDB-6fa4: Antibody derived (Abd-7) small molecule binding to KRAS. -

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Basic information

Entry
Database: PDB / ID: 6fa4
TitleAntibody derived (Abd-7) small molecule binding to KRAS.
Components(GTPase KRas) x 2
KeywordsONCOPROTEIN / Abd-4 / inhibitor / KRAS
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / 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 / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / G protein activity / cytoplasmic side of plasma membrane / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK 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 / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / Ras protein signal transduction / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-D1W / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsQuevedo, C.E. / Cruz-Migoni, A. / Ehebauer, M.T. / Carr, S.B. / Phillips, S.V.E. / Rabbitts, T.H.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust100842/z/12/z United Kingdom
Wellcome Trust099246/z/12/z United Kingdom
Bloodwise12051 United Kingdom
Medical Research Council (United Kingdom)MR/J000612/1 United Kingdom
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
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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
B: GTPase KRas
A: GTPase KRas
C: GTPase KRas
D: GTPase KRas
E: GTPase KRas
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,36423
Polymers118,1276
Non-polymers5,23617
Water2,450136
1
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6394
Polymers19,7011
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0155
Polymers19,6851
Non-polymers1,3294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2323
Polymers19,6851
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6234
Polymers19,6851
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2323
Polymers19,6851
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6234
Polymers19,6851
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.704, 118.619, 157.329
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
11B
21A
12B
22C
13B
23D
14B
24E
15B
25F
16A
26C
17A
27D
18A
28E
19A
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSBA-3 - 1671 - 171
21LYSLYSAB-3 - 1671 - 171
12GLUGLUBA-3 - 1681 - 172
22GLUGLUCC-3 - 1681 - 172
13LYSLYSBA-3 - 1671 - 171
23LYSLYSDD-3 - 1671 - 171
14GLUGLUBA-3 - 1681 - 172
24GLUGLUEE-3 - 1681 - 172
15GLUGLUBA-3 - 1681 - 172
25GLUGLUFF-3 - 1681 - 172
16GLUGLUAB-3 - 1681 - 172
26GLUGLUCC-3 - 1681 - 172
17LYSLYSAB-3 - 1671 - 171
27LYSLYSDD-3 - 1671 - 171
18GLUGLUAB-3 - 1681 - 172
28GLUGLUEE-3 - 1681 - 172
19GLUGLUAB-3 - 1681 - 172
29GLUGLUFF-3 - 1681 - 172
110LYSLYSCC-3 - 1671 - 171
210LYSLYSDD-3 - 1671 - 171
111GLUGLUCC-3 - 1681 - 172
211GLUGLUEE-3 - 1681 - 172
112GLUGLUCC-3 - 1681 - 172
212GLUGLUFF-3 - 1681 - 172
113LYSLYSDD-3 - 1671 - 171
213LYSLYSEE-3 - 1671 - 171
114HISHISDD-3 - 1661 - 170
214HISHISFF-3 - 1661 - 170
115GLUGLUEE-3 - 1681 - 172
215GLUGLUFF-3 - 1681 - 172

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 , 2 types, 6 molecules BACDEF

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


Mass: 19701.209 Da / Num. of mol.: 1 / Mutation: Q61H
Source method: isolated from a genetically manipulated source
Details: KRAS169 Q61H GppNHp / Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116
#2: Protein
GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19685.209 Da / Num. of mol.: 5
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 , 4 types, 153 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-D1W / 6-(2,3-dihydro-1,4-benzodioxin-5-yl)-~{N}-[4-[(dimethylamino)methyl]phenyl]-2-methoxy-pyridin-3-amine


Mass: 391.463 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H25N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 8-15% w/v Polyethylene glycol 3350 and 0.2M Lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.02→65.06 Å / Num. obs: 73612 / % possible obs: 95 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.047 / Rrim(I) all: 0.101 / Net I/σ(I): 10.9
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3782 / CC1/2: 0.671 / Rpim(I) all: 0.311 / Rrim(I) all: 0.669

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCO

5oco


Resolution: 2.02→65.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.382 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23234 3662 5 %RANDOM
Rwork0.20031 ---
obs0.20191 69712 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.905 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.02→65.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 343 136 8554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198696
X-RAY DIFFRACTIONr_bond_other_d0.0020.027890
X-RAY DIFFRACTIONr_angle_refined_deg1.91.97711806
X-RAY DIFFRACTIONr_angle_other_deg1.01318285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.9624.368419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.403151495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6011560
X-RAY DIFFRACTIONr_chiral_restr0.1080.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021788
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_it3.5443.4124124
X-RAY DIFFRACTIONr_mcbond_other3.5423.4124123
X-RAY DIFFRACTIONr_mcangle_it4.9315.0825158
X-RAY DIFFRACTIONr_mcangle_other4.9315.0835159
X-RAY DIFFRACTIONr_scbond_it4.6854.0634572
X-RAY DIFFRACTIONr_scbond_other4.6844.0644573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1675.8616643
X-RAY DIFFRACTIONr_long_range_B_refined9.02540.0279217
X-RAY DIFFRACTIONr_long_range_B_other9.02640.039214
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)
11B105800.08
12A105800.08
21B106360.06
22C106360.06
31B105080.07
32D105080.07
41B105260.08
42E105260.08
51B105980.06
52F105980.06
61A106280.07
62C106280.07
71A105600.07
72D105600.07
81A105100.08
82E105100.08
91A105840.07
92F105840.07
101C105980.05
102D105980.05
111C106520.07
112E106520.07
121C107520.05
122F107520.05
131D106040.07
132E106040.07
141D105940.06
142F105940.06
151E107180.07
152F107180.07
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 300 -
Rwork0.283 5411 -
obs--95.97 %

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