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- PDB-6fa2: Antibody derived (Abd-5) small molecule binding to KRAS. -

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Basic information

Entry
Database: PDB / ID: 6fa2
TitleAntibody derived (Abd-5) small molecule binding to KRAS.
Components(GTPase KRas) x 3
KeywordsONCOPROTEIN / Abd-5 / inhibitor / KRAS
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / 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 / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / positive regulation of glial cell proliferation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / 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 / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / 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 / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / mitochondrial outer membrane / negative regulation of neuron apoptotic process / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-D2W / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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)122,02624
Polymers115,9666
Non-polymers6,06018
Water50428
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0344
Polymers19,0231
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3664
Polymers19,3561
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5294
Polymers19,5191
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3664
Polymers19,3561
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3664
Polymers19,3561
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3664
Polymers19,3561
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.230, 117.215, 156.446
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 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETHISHISAA1 - 1661 - 166
21METMETHISHISBB1 - 1664 - 169
12METMETLYSLYSAA1 - 1671 - 167
22METMETLYSLYSCC1 - 1675 - 171
13METMETLYSLYSAA1 - 1671 - 167
23METMETLYSLYSDD1 - 1674 - 170
14METMETLYSLYSAA1 - 1671 - 167
24METMETLYSLYSEE1 - 1674 - 170
15METMETLYSLYSAA1 - 1671 - 167
25METMETLYSLYSFF1 - 1674 - 170
16PHEPHELYSLYSBB-2 - 1671 - 170
26PHEPHELYSLYSCC-2 - 1672 - 171
17PHEPHELYSLYSBB-2 - 1671 - 170
27PHEPHELYSLYSDD-2 - 1671 - 170
18PHEPHELYSLYSBB-2 - 1671 - 170
28PHEPHELYSLYSEE-2 - 1671 - 170
19PHEPHELYSLYSBB-2 - 1671 - 170
29PHEPHELYSLYSFF-2 - 1671 - 170
110PHEPHELYSLYSCC-2 - 1672 - 171
210PHEPHELYSLYSDD-2 - 1671 - 170
111PHEPHELYSLYSCC-2 - 1672 - 171
211PHEPHELYSLYSEE-2 - 1671 - 170
112PHEPHELYSLYSCC-2 - 1672 - 171
212PHEPHELYSLYSFF-2 - 1671 - 170
113PHEPHELYSLYSDD-2 - 1671 - 170
213PHEPHELYSLYSEE-2 - 1671 - 170
114PHEPHELYSLYSDD-2 - 1671 - 170
214PHEPHELYSLYSFF-2 - 1671 - 170
115PHEPHELYSLYSEE-2 - 1671 - 170
215PHEPHELYSLYSFF-2 - 1671 - 170

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 , 3 types, 6 molecules ABDEFC

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


Mass: 19023.482 Da / Num. of mol.: 1 / 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
#2: Protein
GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19355.840 Da / Num. of mol.: 4 / 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
#3: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19519.014 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) / Strain (production host): KRAS, KRAS2, RASK2 / References: UniProt: P01116

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Non-polymers , 4 types, 46 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical
ChemComp-D2W / 4-[2-(dimethylamino)ethoxy]-~{N}-[[(3~{R})-5-(6-methoxypyridin-2-yl)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]benzamide


Mass: 463.526 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H29N3O5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→93.81 Å / Num. obs: 36640 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.033 / Rrim(I) all: 0.067 / Net I/σ(I): 19.1
Reflection shellResolution: 2.6→2.72 Å / CC1/2: 0.748 / Rpim(I) all: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→93.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.101 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.023 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23301 1723 4.7 %RANDOM
Rwork0.2032 ---
obs0.20455 34830 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.248 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å20 Å2
2--9.14 Å2-0 Å2
3----5.9 Å2
Refinement stepCycle: 1 / Resolution: 2.6→93.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7700 0 402 28 8130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198262
X-RAY DIFFRACTIONr_bond_other_d0.0020.027488
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.01311196
X-RAY DIFFRACTIONr_angle_other_deg0.947317322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09424.433379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.904151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8411551
X-RAY DIFFRACTIONr_chiral_restr0.0820.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021680
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_it4.9596.0253912
X-RAY DIFFRACTIONr_mcbond_other4.9586.0243911
X-RAY DIFFRACTIONr_mcangle_it7.5049.0154867
X-RAY DIFFRACTIONr_mcangle_other7.5049.0164868
X-RAY DIFFRACTIONr_scbond_it6.0846.9864350
X-RAY DIFFRACTIONr_scbond_other6.0836.9864351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.57710.1846327
X-RAY DIFFRACTIONr_long_range_B_refined12.23371.7558917
X-RAY DIFFRACTIONr_long_range_B_other12.23271.7548918
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)
11A102000.06
12B102000.06
21A100200.05
22C100200.05
31A98300.05
32D98300.05
41A99400.06
42E99400.06
51A96680.06
52F96680.06
61B102180.04
62C102180.04
71B99840.04
72D99840.04
81B101700.06
82E101700.06
91B99280.05
92F99280.05
101C99420.04
102D99420.04
111C99940.05
112E99940.05
121C98380.05
122F98380.05
131D98560.05
132E98560.05
141D99300.04
142F99300.04
151E97920.05
152F97920.05
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 126 -
Rwork0.394 2543 -
obs--99.93 %

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