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- PDB-9ggw: Human KRas4A (GDP) in complex with compound 16 -

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Basic information

Entry
Database: PDB / ID: 9ggw
TitleHuman KRas4A (GDP) in complex with compound 16
ComponentsGTPase KRas
KeywordsCELL CYCLE / RAS / GTPase / inhibitor
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / skeletal muscle cell differentiation / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / RAF activation / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / 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 / positive regulation of cellular senescence / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSchuettelkopf, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Reversible Small Molecule Multivariant Ras Inhibitors Display Tunable Affinity for the Active and Inactive Forms of Ras.
Authors: Parry, C.W. / Pellicano, F. / Schuttelkopf, A.W. / Beyer, K.S. / Bower, J. / Bryson, A. / Cameron, K. / Cerutti, N.M. / Clark, J.P. / Davidson, S.C. / Davies, K. / Drysdale, M.J. / Engelman, ...Authors: Parry, C.W. / Pellicano, F. / Schuttelkopf, A.W. / Beyer, K.S. / Bower, J. / Bryson, A. / Cameron, K. / Cerutti, N.M. / Clark, J.P. / Davidson, S.C. / Davies, K. / Drysdale, M.J. / Engelman, J. / Estevan-Barber, A. / Gohlke, A. / Gray, C.H. / Guthy, D.A. / Hong, M. / Hopkins, A. / Hutchinson, L.D. / Konczal, J. / Maira, M. / McArthur, D. / Mezna, M. / McKinnon, H. / Nepravishta, R. / Ostermann, N. / Pasquali, C.C. / Pollock, K. / Pugliese, A. / Rooney, N. / Schmiedeberg, N. / Shaw, P. / Velez-Vega, C. / West, C. / West, R. / Zecri, F. / Taylor, J.B.
History
DepositionAug 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,40610
Polymers39,2142
Non-polymers2,1918
Water2,342130
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7035
Polymers19,6071
Non-polymers1,0964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7035
Polymers19,6071
Non-polymers1,0964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.065, 41.054, 209.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 19607.078 Da / Num. of mol.: 2 / Mutation: C118S
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, small monomeric GTPase

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Non-polymers , 5 types, 138 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1ILA / 11-(4-aminocyclohexyl)-16-chloro-1,15-dihydroxy-10,10-dioxo-10lambda6-thia-2,11lambda6-diaza-1lambda6,15lambda6-diphospha-3-phosphoniapentacyclo[7.5.1.01,15.03,15.013,15]hexadecan-12-one


Mass: 566.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30ClN4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 25% PEG 8000, 300 mM LiCl, 100 mM bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97998 Å / Relative weight: 1
ReflectionResolution: 1.818→209.005 Å / Num. obs: 29802 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.088 / Rrim(I) all: 0.166 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.818-1.8496.50.91315010.7370.5291.00199.9
4.934-209.0055.80.05116530.9980.0310.05999.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→104.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.393 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1496 5 %RANDOM
Rwork0.2342 ---
obs0.2358 28292 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43 Å2 / Biso mean: 23.757 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---2.41 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.82→104.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 140 130 2959
Biso mean--22.67 26.8 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132867
X-RAY DIFFRACTIONr_bond_other_d0.0350.0182614
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.7283890
X-RAY DIFFRACTIONr_angle_other_deg2.4081.6396054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7555331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35322160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4191523
X-RAY DIFFRACTIONr_chiral_restr0.1290.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023131
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02604
X-RAY DIFFRACTIONr_mcbond_it0.2770.3341333
X-RAY DIFFRACTIONr_mcbond_other0.2770.3341332
X-RAY DIFFRACTIONr_mcangle_it0.4910.4991661
LS refinement shellResolution: 1.82→1.865 Å
RfactorNum. reflection% reflection
Rfree0.298 103 -
Rwork0.312 2090 -
obs--99.86 %
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)
11.0448-0.07670.22481.12640.14411.933-0.02270.0369-0.0458-0.1846-0.00970.04280.05710.00550.03230.03620.00170.00720.190.00540.216511.07134.663239.2626
21.66840.31240.07350.1982-0.10660.5987-0.00670.0110.01480.04650.0065-0.01-0.0364-0.0010.00010.36260.01360.01350.196-0.00360.20614.6543-2.308-11.4958
30.00750.00380.06380.07340.02180.6602-0.00260.00910.0167-0.11220.00180.0117-0.0622-0.00860.00080.1786-0.00220.02340.26570.00380.290614.92794.728320.1931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 168
2X-RAY DIFFRACTION2B1 - 169

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