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- PDB-9bak: Crystal structure of GDP-bound human K-RAS in a covalent complex ... -

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Basic information

Entry
Database: PDB / ID: 9bak
TitleCrystal structure of GDP-bound human K-RAS in a covalent complex with aryl sulfonyl fluoride compounds.
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / KRAS / cancer / GTPase / covalent inhibitor / sulfonyl fluoride
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 / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / 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 / 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:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / 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 / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / Insulin receptor signalling cascade / 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 / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / 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 / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / 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: 1.67 Å
AuthorsLandgraf, A.D. / Brenner, R.J. / Ghozayel, M.K. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA264471 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
CitationJournal: Chemmedchem / Year: 2025
Title: Small-Molecule KRAS Inhibitors by Tyrosine Covalent Bond Formation.
Authors: Landgraf, A.D. / Brenner, R. / Ghozayel, M.K. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Isoform 2B of GTPase KRas
D: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09016
Polymers77,0234
Non-polymers3,06712
Water11,512639
1
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0234
Polymers19,2561
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0234
Polymers19,2561
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0234
Polymers19,2561
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0234
Polymers19,2561
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.867, 83.885, 104.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 19255.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116, small monomeric GTPase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-WN3 / 3-[bis(oxidanylidene)-$l^{5}-sulfanyl]-~{N}-pyridazin-3-yl-benzenesulfonamide


Mass: 299.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium chloride 0.2 M and PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.67→104.69 Å / Num. obs: 69748 / % possible obs: 96.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.97 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Rsym value: 0.089 / Net I/σ(I): 9
Reflection shellResolution: 1.67→1.7 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 12897 / CC1/2: 0.596 / Rpim(I) all: 0.535 / Rrim(I) all: 1.036 / Rsym value: 0.885 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→52.34 Å / Cross valid method: FREE R-VALUE / σ(F): 20.99 / Phase error: 34.3353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2886 3326 5.1 %
Rwork0.2703 61864 -
obs0.2743 65190 90.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.41 Å2
Refinement stepCycle: LAST / Resolution: 1.67→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 192 639 6141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335615
X-RAY DIFFRACTIONf_angle_d0.69287608
X-RAY DIFFRACTIONf_chiral_restr0.0446836
X-RAY DIFFRACTIONf_plane_restr0.0045967
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.28381830.30453324X-RAY DIFFRACTION91.65
1.69-1.730.31271480.30473361X-RAY DIFFRACTION92.59
1.73-1.760.29771620.3183283X-RAY DIFFRACTION92.22
1.76-1.790.35861500.32633397X-RAY DIFFRACTION92.97
1.79-1.830.42481430.37033256X-RAY DIFFRACTION91.38
1.83-1.880.48051160.51712045X-RAY DIFFRACTION56.21
1.88-1.920.81651210.78172057X-RAY DIFFRACTION57.43
1.92-1.980.38491070.36181991X-RAY DIFFRACTION54.56
1.98-2.030.25021730.24693299X-RAY DIFFRACTION92.98
2.03-2.10.25321850.22973398X-RAY DIFFRACTION93.02
2.1-2.170.26921870.22523332X-RAY DIFFRACTION92.94
2.17-2.260.40451210.37062122X-RAY DIFFRACTION58.36
2.26-2.360.30621400.28613222X-RAY DIFFRACTION90.25
2.36-2.490.25492130.21623378X-RAY DIFFRACTION92.9
2.49-2.640.26091570.22493412X-RAY DIFFRACTION94.52
2.65-2.850.21561760.22323434X-RAY DIFFRACTION94.29
2.85-3.140.24671980.20513377X-RAY DIFFRACTION93.73
3.14-3.590.22352000.18393445X-RAY DIFFRACTION93.82
3.59-4.520.20891860.20483318X-RAY DIFFRACTION90.9
4.52-52.340.1951890.19093484X-RAY DIFFRACTION94.26
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)
11.544799483241.37185385435-0.7227776993492.16700165434-0.8388276894451.36895950167-0.0994354908420.3029983563180.1698410609870.177911188216-0.02436900772230.184280164836-0.437233511198-0.3592083340690.1911170248040.1879393765710.04883149532950.004454617055530.273827613499-0.05268230538720.15916589648912.2587308802-29.240179460445.1838408905
20.625257808052-0.03247329344020.1151582388141.929165486740.7844102936980.80405096315-0.0240055759481-0.1228961878210.00546407885438-0.2419786723060.156950127667-0.0221945800974-0.0768115406834-0.0239229144324-0.001955826593020.120715086459-0.0546335971-0.03039960242290.276573525661-0.02256323104880.073586043237123.178352815-32.966221397530.6550555421
32.03352110565-0.206979094173-1.324313473750.9055303136370.1156792600972.30455142076-0.04201546715510.5183945781860.349101127511-0.4673934614460.196318501435-0.0263318932502-0.0407254703838-0.331682611045-0.1004353786590.121799235841-0.02078480388880.02344191851310.111180194280.03688117349640.2382419592827.3310242669-18.924153374333.9419518351
42.244472767350.7842781172781.059722837092.134090876320.4846812473032.795979978-0.13145145898-0.0701561130409-0.212480983185-0.1898242694630.0547390533877-0.121353038441-0.1003767270030.009982158890530.1300430851710.0889364680467-0.0200222294353-0.005034213056110.1194783212850.003137796726590.10886231194611.1123117539-12.62738393347.61199568501
51.015356169940.731626988770.551165964845.78055342784-0.131232211631.61514056858-0.0858110165127-0.4558795575450.1504009894370.1015285342790.08676956171130.786798762374-0.151422056901-0.2831083883410.09125458559920.1022566463150.0200885544235-0.03163992277650.338966763333-0.01828509891860.1183566133565.94234536393-7.4290933051220.4642739422
61.410834016780.396477027366-0.02126632131682.87486017934-0.3343357095682.378234990380.11982216381-0.25350000988-0.122324811265-0.06871445657730.008808234573270.0160262297604-0.01305198074510.0547088508802-0.1177723393630.1037948520470.017635518058-0.006493733213740.2887070207470.02616836028360.06274703539315.4684144975-12.237688402121.3938554368
70.627880825835-0.322455530690.3162745638832.245299586930.07119729045090.4082022332530.06140186510170.183439802201-0.0211051050538-0.3864753294790.00072252667757-0.2488848384820.2219559381090.252905371102-0.02026940203010.1687616531470.05888016063130.01682350677440.169326407156-0.0413457881130.07119410429069.6768058292930.50605760667.34389194214
82.46680563755-0.9756216272390.9858435007871.31689688196-0.6525232111471.554508008750.0472178256124-0.0478807529359-0.103796161242-0.1907272755150.1383325876780.0009798390415230.00090964252528-0.0208937706165-0.09614822631820.1171542417550.0307907132611-0.03952429082280.139668180810.009420418232330.1312192763012.961210913724.14070915767.52624636823
91.697678729340.258571246107-0.3507469481852.035142720880.2737790691622.237435431580.096033192026-0.1665298286490.001981624505450.0209917474812-0.1729570986720.132545457780.100966640544-0.02260375447480.02774324460970.0926260551958-0.0480490267266-0.01490479285030.08095540349490.01489942893850.07878636694225.4044754331633.224934461721.6733013552
102.510706177730.9273132555850.2232228057515.145409902940.4180589595374.07123622598-0.015733674357-0.150100044843-0.2329806489740.3693220578280.0236330692251-0.02258714877970.206815101305-0.270195967819-0.01116765151070.163126625725-0.0800336200015-0.0168519894320.4363457588770.05233847637160.1387146948479.382518590319.071183445718.3909984764
110.805452538645-0.4350723514510.08960484560061.681434024270.3580479952781.665627018910.061383185756-0.13927750309-0.0483120712850.3843192674370.0726393223030.0837812364427-0.2381792125960.2361854429380.1276400526340.179177039766-0.0777670340020.01886493517030.3081342190690.02471092437820.0283665611925-4.044202984038.537088668445.5630691599
120.881822914484-0.246581405957-0.2921420026471.18054437989-0.2491970986111.313470859260.118871970561-0.0920304590560.106892440191-0.02921732276960.247456384315-0.0250076616656-0.1687422054760.0335750492329-0.03742824161410.2152069189980.01184986536550.08052685823980.308212875214-0.02754812108410.124876998912-8.6040530349816.639122010645.8044235903
130.871433829127-0.145275888268-0.1694723828035.198358450820.9214966776871.695444122190.1803683930130.154594419958-0.1131210395050.0923051060091-0.06358730824730.2098938602660.13071848478-0.396817441047-0.02155930007820.0825272235344-0.00521286326175-0.03329391699590.294849076585-0.02653741711180.095564816859-10.74473791635.7193057044533.5543097866
142.83427551609-1.30706125885-0.08781466442264.51407927450.9767115376461.820338543010.1214847919720.1012788655510.108003327029-0.393886295867-0.2214641688840.234836601723-0.167214069361-0.301236940740.0520405928410.176898078074-0.0791711408199-0.0428519555070.2259495736030.04600272509410.0246251384199-11.94001026839.8329811769432.1963994056
154.12352937639-2.792725128931.418192840215.21252927935-0.1270707498555.38852712804-0.003145411781140.170076169373-0.0298692847098-0.4595110952130.1763699375930.0337379404760.5559131151170.0559152582619-0.2358320373930.254237313078-0.108563281123-0.0812358003090.3205266957960.002167230301310.161564795838-8.42404879478.7893268449522.1768553801
161.24883201143-1.517780653470.7412244574243.4213878375-0.9135287196771.10910004617-0.1770563245720.05365344935220.0334712129327-0.006499993688090.0337980764458-0.2362028412680.111527378829-0.2025071321210.0801230683170.104494137699-0.06180007277450.06019358619260.214007336896-0.001910350249330.0957314080496-0.10429885321613.772325865734.3106087347
172.68030933607-1.94216496953-0.1373145177523.18674372055-1.164125070251.1211352371-0.2028769886480.06888273571920.4334736718050.5134518965830.206527574679-0.208221332065-0.151903160552-0.200747119666-0.06307666752020.1837590782410.07599093228010.01856202166020.2356070693610.04972381228890.050925492070826.5989309865-26.77399922742.6896145029
180.9424713209610.1513352463340.1262228781250.8300341509150.7585911348031.45013423840.035754883511-0.10984542505-0.08767440800590.229600510711-0.257592717705-0.166778896537-0.02072141377190.1174296633590.09036014738980.1881890641490.0833984533804-0.003708250679030.3841138187050.08473130586360.095337122695528.9059267034-25.910591935446.3385230792
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 58 through 74 )CI58 - 7458 - 74
22chain 'C' and (resid 75 through 151 )CI75 - 15175 - 151
33chain 'C' and (resid 152 through 167 )CI152 - 167152 - 167
44chain 'D' and (resid 1 through 83 )DM1 - 831 - 83
55chain 'D' and (resid 84 through 126 )DM84 - 12684 - 126
66chain 'D' and (resid 127 through 166 )DM127 - 166127 - 166
77chain 'A' and (resid 1 through 37 )AA1 - 371 - 37
88chain 'A' and (resid 38 through 74 )AA38 - 7438 - 74
99chain 'A' and (resid 75 through 151 )AA75 - 15175 - 151
1010chain 'A' and (resid 152 through 167 )AA152 - 167152 - 167
1111chain 'B' and (resid 1 through 37 )BE1 - 371 - 37
1212chain 'B' and (resid 38 through 74 )BE38 - 7438 - 74
1313chain 'B' and (resid 75 through 92 )BE75 - 9275 - 92
1414chain 'B' and (resid 93 through 126 )BE93 - 12693 - 126
1515chain 'B' and (resid 127 through 137 )BE127 - 137127 - 137
1616chain 'B' and (resid 138 through 166 )BE138 - 166138 - 166
1717chain 'C' and (resid 1 through 25 )CI1 - 251 - 25
1818chain 'C' and (resid 26 through 57 )CI26 - 5726 - 57

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