PDB-9p46: Crystal structure of HRAS-G12D/Q95H (GMPPNP-bound) in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 9p46

Title

Crystal structure of HRAS-G12D/Q95H (GMPPNP-bound) in complex with BBO-11818

Components

GTPase HRas

Keywords

ONCOPROTEIN / HRAS / RAS / H-ras / inhibitor / BBO-11818 / BBO11818 / BBO / TheRas / BridgeBio / ONCOPROTEIN-INHIBITOR complex

Function / homology

Function and homology information

phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / adipose tissue development / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / 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 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 / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / 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 / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / small monomeric GTPase / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / RAF activation / Signaling by ERBB2 TMD/JMD mutants / cellular response to gamma radiation / 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 / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / chemotaxis / 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 / cellular senescence / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway / MAPK cascade / regulation of cell population proliferation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.02 Å

Authors

Chan, A.H. / Bratcher, D.R. / Simanshu, D.K.

Funding support

United States, 1items

Citation

Journal: Cancer Discov / Year: 2025
Title: Discovery of BBO-11818, a Potent and Selective Non-covalent Inhibitor of (ON) and (OFF) KRAS with Activity Against Multiple Oncogenic Mutants
Authors: Maciag, A.E. / Chan, A.H. / Simanshu, D.K. / Beltran, P.J.

History

Deposition	Jun 16, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9p46.cif.gz	155 KB	Display	PDBx/mmCIF format
PDB format	pdb9p46.ent.gz		Display	PDB format
PDBx/mmJSON format	9p46.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9p46_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9p46_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9p46_validation.xml.gz	21 KB	Display
Data in CIF	9p46_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p4/9p46 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/9p46	HTTPS FTP

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Related structure data

Related structure data	9p44C 9p45C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#148 - Apr 2012 Ras Protein similarity (50) #195 - Mar 2016 RAF Protein Kinases similarity (49) #126 - Jun 2010 Epidermal Growth Factor similarity (6) #245 - May 2020 Spliceosomes similarity (4) #122 - Feb 2010 Enhanceosome similarity (5) #43 - Jul 2003 Src Tyrosine Kinase similarity (6) #60 - Dec 2004 Ubiquitin similarity (6) #194 - Feb 2016 Designer Insulins similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (2) #182 - Feb 2015 Insulin receptor similarity (1) #68 - Aug 2005 Neurotrophins similarity (3) #44 - Aug 2003 Calmodulin similarity (2) #222 - Jun 2018 Proteins and Nanoparticles similarity (2) #14 - Feb 2001 Insulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (2) #28 - Apr 2002 Anthrax Toxin similarity (2) #81 - Sep 2006 Elongation Factors similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#148 - Apr 2012
Ras Protein
similarity (50)
#195 - Mar 2016
RAF Protein Kinases
similarity (49)
#126 - Jun 2010
Epidermal Growth Factor
similarity (6)
#245 - May 2020
Spliceosomes
similarity (4)
#122 - Feb 2010
Enhanceosome
similarity (5)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (6)
#60 - Dec 2004
Ubiquitin
similarity (6)
#194 - Feb 2016
Designer Insulins
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (2)
#182 - Feb 2015
Insulin receptor
similarity (1)
#68 - Aug 2005
Neurotrophins
similarity (3)
#44 - Aug 2003
Calmodulin
similarity (2)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (2)
#14 - Feb 2001
Insulin
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (2)
#28 - Apr 2002
Anthrax Toxin
similarity (2)
#81 - Sep 2006
Elongation Factors
similarity (1)
#52 - Apr 2004
Growth Hormone
similarity (1)
#236 - Aug 2019
Cyclin and Cyclin-dependent Kinase
similarity (1)

Deposited unit

A: GTPase HRas

B: GTPase HRas

hetero molecules

41.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTPase HRas

hetero molecules

defined by author&software
Evidence: gel filtration
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GTPase HRas

hetero molecules

defined by author&software
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.330, 106.330, 121.410
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

#1: Protein	GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras Mass: 19383.766 Da / Num. of mol.: 2 / Mutation: G12D, Q95H, C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112, small monomeric GTPase
#2: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃ Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-A1CG4 / methyl (3S)-3-{[(7P)-7-(2-amino-3-cyano-7-fluoro-1-benzothiophen-4-yl)-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-6-(trifluoromethyl)quinazolin-4-yl](ethyl)amino}pyrrolidine-1-carboxylate Mass: 733.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₃F₆N₇O₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350, 0.2 M MgCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors

Radiation

Monochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.02→29.76 Å / Num. obs: 26915 / % possible obs: 99.6 % / Redundancy: 11.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.212 / R_rim(I) all: 0.222 / Net I/σ(I): 10.07

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.02-2.08	1.205	2.03	1905	0.608	1.26	1
2.08-2.13	0.978		1904	0.708	1.022	1
2.13-2.2	0.772		1839	0.798	0.806	1
2.2-2.26	0.643		1817	0.846	0.673	1
2.26-2.34	0.583		1759	0.869	0.61	1
2.34-2.42	0.526		1691	0.904	0.551	1
2.42-2.51	0.467		1637	0.939	0.489	1
2.51-2.61	0.41		1571	0.948	0.429	1
2.61-2.73	0.35		1543	0.977	0.365	1
2.73-2.86	0.305		1446	0.984	0.318	1
2.86-3.02	0.246		1397	0.982	0.257	1
3.02-3.2	0.193		1320	0.997	0.202	1
3.2-3.42	0.145		1248	0.994	0.152	1
3.42-3.7	0.118		1169	0.995	0.124	1
3.7-4.05	0.093		1084	0.997	0.097	1
4.05-4.53	0.077		987	0.998	0.08	1
4.53-5.23	0.074		887	0.998	0.078	1
5.23-6.4	0.096		758	0.997	0.1	1
6.4-9.05	0.07		605	0.997	0.074	1
9.05-29.76	0.047		348	0.998	0.05	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.02→29.76 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2275	2692	10 %
R_work	0.1806	-	-
obs	0.1853	26915	99.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.02→29.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2618	0	168	229	3015

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2839
X-RAY DIFFRACTION	f_angle_d	0.915	3864
X-RAY DIFFRACTION	f_dihedral_angle_d	15.708	1108
X-RAY DIFFRACTION	f_chiral_restr	0.05	420
X-RAY DIFFRACTION	f_plane_restr	0.007	480

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.02-2.06	0.285	135	0.2517	1211	X-RAY DIFFRACTION	97
2.06-2.1	0.2736	139	0.2242	1248	X-RAY DIFFRACTION	100
2.1-2.14	0.2461	138	0.2175	1249	X-RAY DIFFRACTION	100
2.14-2.19	0.2804	139	0.2025	1246	X-RAY DIFFRACTION	100
2.19-2.24	0.2505	139	0.1941	1254	X-RAY DIFFRACTION	100
2.24-2.3	0.2241	139	0.1801	1251	X-RAY DIFFRACTION	100
2.3-2.36	0.2603	140	0.1838	1265	X-RAY DIFFRACTION	100
2.36-2.43	0.2672	140	0.1929	1260	X-RAY DIFFRACTION	100
2.43-2.51	0.2301	140	0.1807	1254	X-RAY DIFFRACTION	100
2.51-2.6	0.2309	141	0.1804	1274	X-RAY DIFFRACTION	100
2.6-2.7	0.2508	139	0.1746	1255	X-RAY DIFFRACTION	100
2.7-2.82	0.2328	143	0.1776	1282	X-RAY DIFFRACTION	100
2.82-2.97	0.2077	141	0.1776	1265	X-RAY DIFFRACTION	100
2.97-3.16	0.2151	142	0.1657	1286	X-RAY DIFFRACTION	100
3.16-3.4	0.217	143	0.1529	1282	X-RAY DIFFRACTION	100
3.4-3.74	0.205	144	0.1626	1293	X-RAY DIFFRACTION	100
3.74-4.28	0.196	145	0.1518	1310	X-RAY DIFFRACTION	100
4.28-5.39	0.213	148	0.1656	1334	X-RAY DIFFRACTION	100
5.39-29.76	0.2306	157	0.2296	1404	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.4173	0.0765	0.3926	1.2541	0.3492	1.046	-0.0022	0.0809	-0.2725	-0.021	0.0824	-0.2299	0.138	0.2392	-0.0654	0.1633	0.0295	0.0105	0.1485	-0.0048	0.177	70.8376	-15.3333	-14.0309
2	1.9042	-0.2924	1.4282	1.4092	1.23	2.671	0.0633	0.1134	0.1354	0.0611	-0.0902	-0.2975	0.0807	0.5447	0.086	0.2231	-0.0177	0.0046	0.243	0.0122	0.2552	76.713	-15.975	-13.7203
3	1.8519	-0.3741	1.4918	0.9116	-0.4937	2.3761	0.2062	0.1166	-0.205	-0.0174	-0.0496	-0.03	0.206	0.1036	-0.127	0.185	0.0172	0.0024	0.203	-0.0091	0.1774	65.0571	-18.1722	-21.3773
4	0.9363	0.7542	0.3261	1.3832	0.3472	1.3248	-0.0397	-0.0097	0.0794	0.1229	-0.0308	0.0345	-0.0729	-0.0289	0.0809	0.1523	0.0108	0.0011	0.1249	0.0238	0.1541	60.5978	-5.8908	-14.578
5	2.1484	-0.117	0.2943	1.1535	0.3675	1.2529	-0.17	-0.1212	0.2237	0.2072	0.0246	-0.1381	-0.1224	-0.023	0.1116	0.2501	0.0148	-0.0116	0.1169	0.0197	0.1901	62.2435	-4.4357	-5.5369
6	3.0582	0.5281	0.3814	2.6138	0.0268	2.6027	0.0165	-0.3628	-0.4147	0.2643	-0.0812	0.0227	0.3593	-0.3616	0.0435	0.2488	-0.0217	0.0227	0.1668	-0.0041	0.1701	62.4421	-19.0411	-5.7076
7	1.7902	0.1953	-0.0349	2.8324	0.2587	1.0071	-0.0726	0.1232	0.1309	-0.1405	0.031	0.3296	-0.2099	-0.2189	0.0267	0.1793	0.0473	0.0132	0.1681	-0.0132	0.1772	32.6053	12.5654	-17.375
8	0.3017	-0.4807	-0.2788	1.0268	0.3776	2.33	-0.04	0.1387	0.0683	-0.2271	-0.2029	0.4186	-0.1424	-0.1208	0.2168	0.2005	0.0765	-0.0346	0.2831	-0.0242	0.2561	29.1237	16.1166	-16.2464
9	2.0499	-0.1545	-0.7224	1.3634	0.588	1.8128	0.2001	0.3216	0.1254	-0.2661	-0.1773	0.0782	-0.4102	-0.2448	-0.0348	0.2472	0.0624	0.0218	0.2072	-0.0044	0.1623	43.6527	12.3293	-29.8702
10	1.0124	0.6929	-0.4874	1.4218	-0.0551	1.4563	0.0619	-0.0865	-0.0085	0.0777	-0.1215	0.0674	-0.0284	0.0178	0.0754	0.1529	0.0085	0.0232	0.1482	-0.019	0.1366	43.0241	3.2826	-15.8626
11	2.1615	0.2498	0.2155	1.1382	-0.2351	1.143	-0.1281	-0.0789	-0.2273	0.2649	0.053	0.1296	0.0052	-0.2075	0.0114	0.2206	0.0069	0.0563	0.1669	-0.0312	0.1781	39.5845	1.8841	-7.2486
12	4.4296	0.1059	-0.1901	2.5068	-0.838	4.3889	0.1295	-0.3016	0.2604	0.3401	-0.3268	0.0868	-0.1443	0.3464	0.1232	0.2295	0.0664	0.0785	0.2039	-0.014	0.1914	39.0371	16.4063	-7.84

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 74 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 126 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 127 through 151 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 152 through 168 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 25 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 57 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 74 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 75 through 126 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 127 through 151 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 152 through 168 )

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi