PDB-9p45: Crystal structure of KRAS-G12D (GMPPNP-bound) in complex with BBO...

ID or keywords:

Entry

Database: PDB / ID: 9p45

Title

Crystal structure of KRAS-G12D (GMPPNP-bound) in complex with BBO-11818

Components

Isoform 2B of GTPase KRas

Keywords

ONCOPROTEIN/INHIBITOR / KRAS / RAS / K-ras / KRAS4b / inhibitor / BBO-11818 / BBO11818 / BBO / TheRas / BridgeBio / oncoprotein / ONCOPROTEIN-INHIBITOR complex

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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 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	9p45.cif.gz	121.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9p45.ent.gz		Display	PDB format
PDBx/mmJSON format	9p45.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9p45_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9p45_full_validation.pdf.gz	1 MB	Display
Data in XML	9p45_validation.xml.gz	12.9 KB	Display
Data in CIF	9p45_validation.cif.gz	17.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p4/9p45 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/9p45	HTTPS FTP

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Related structure data

Related structure data	9p44C 9p46C 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 (48) #195 - Mar 2016 RAF Protein Kinases similarity (47) #126 - Jun 2010 Epidermal Growth Factor similarity (6) #122 - Feb 2010 Enhanceosome similarity (7) #43 - Jul 2003 Src Tyrosine Kinase similarity (6) #194 - Feb 2016 Designer Insulins similarity (1) #245 - May 2020 Spliceosomes similarity (3) #60 - Dec 2004 Ubiquitin similarity (5) #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 (48)
#195 - Mar 2016
RAF Protein Kinases
similarity (47)
#126 - Jun 2010
Epidermal Growth Factor
similarity (6)
#122 - Feb 2010
Enhanceosome
similarity (7)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (6)
#194 - Feb 2016
Designer Insulins
similarity (1)
#245 - May 2020
Spliceosomes
similarity (3)
#60 - Dec 2004
Ubiquitin
similarity (5)
#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: Isoform 2B of GTPase KRas

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.610, 79.610, 57.810
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-391- HOH
2	1	A-428- HOH
3	1	A-478- HOH

#1: Protein	Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras Mass: 19370.781 Da / Num. of mol.: 1 / Mutation: G12D, 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
#2: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₃F₆N₇O₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.36 Å³/Da / Density % sol: 47.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6, 45% PEG 200, 0.05 M CaCl2

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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: 0.97934 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 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: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 1.35→40.33 Å / Num. obs: 41119 / % possible obs: 99.8 % / Redundancy: 20.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.094 / R_rim(I) all: 0.096 / Net I/σ(I): 17.9

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
1.35-1.39	1.241	1.94	2908	0.338	1.301	1
1.39-1.42	1.142		2926	0.476	1.184	1
1.42-1.47	1.058		2832	0.708	1.087	1
1.47-1.51	0.896		2763	0.858	0.917	1
1.51-1.56	0.734		2712	0.918	0.751	1
1.56-1.62	0.608		2582	0.942	0.622	1
1.62-1.68	0.502		2497	0.968	0.513	1
1.68-1.74	0.411		2428	0.977	0.421	1
1.74-1.82	0.317		2336	0.99	0.325	1
1.82-1.91	0.232		2225	0.994	0.238	1
1.91-2.01	0.169		2119	0.997	0.173	1
2.01-2.14	0.128		2028	0.998	0.131	1
2.14-2.28	0.104		1899	0.998	0.107	1
2.28-2.47	0.085		1778	0.999	0.087	1
2.47-2.7	0.074		1642	0.999	0.076	1
2.7-3.02	0.063		1507	0.999	0.065	1
3.02-3.49	0.054		1331	0.999	0.056	1
3.49-4.27	0.05		1147	0.998	0.051	1
4.27-6.04	0.05		913	0.999	0.051	1
6.04-40.33	0.051		546	0.999	0.053	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: 1.35→40.33 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1937	4112	10 %
R_work	0.1749	-	-
obs	0.1768	41116	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.35→40.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1341	0	85	178	1604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1466
X-RAY DIFFRACTION	f_angle_d	1.1	2000
X-RAY DIFFRACTION	f_dihedral_angle_d	15.61	581
X-RAY DIFFRACTION	f_chiral_restr	0.074	218
X-RAY DIFFRACTION	f_plane_restr	0.01	249

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 (%)
1.35-1.37	0.3661	133	0.3431	1192	X-RAY DIFFRACTION	95
1.37-1.38	0.2977	136	0.3275	1227	X-RAY DIFFRACTION	99
1.38-1.4	0.3209	139	0.3039	1261	X-RAY DIFFRACTION	100
1.4-1.42	0.2891	141	0.2844	1266	X-RAY DIFFRACTION	100
1.42-1.44	0.301	139	0.2813	1251	X-RAY DIFFRACTION	100
1.44-1.46	0.2815	139	0.2625	1248	X-RAY DIFFRACTION	100
1.46-1.48	0.2511	141	0.2633	1276	X-RAY DIFFRACTION	100
1.48-1.5	0.2565	139	0.2288	1247	X-RAY DIFFRACTION	100
1.5-1.53	0.2475	142	0.222	1273	X-RAY DIFFRACTION	100
1.53-1.56	0.2553	138	0.2	1246	X-RAY DIFFRACTION	100
1.56-1.58	0.1905	142	0.1977	1282	X-RAY DIFFRACTION	100
1.58-1.61	0.2427	142	0.1925	1267	X-RAY DIFFRACTION	100
1.61-1.65	0.2047	140	0.1912	1256	X-RAY DIFFRACTION	100
1.65-1.68	0.2091	139	0.1802	1255	X-RAY DIFFRACTION	100
1.68-1.72	0.2015	141	0.1796	1272	X-RAY DIFFRACTION	100
1.72-1.77	0.1942	142	0.1787	1270	X-RAY DIFFRACTION	100
1.77-1.81	0.207	142	0.1733	1284	X-RAY DIFFRACTION	100
1.81-1.87	0.189	140	0.1647	1261	X-RAY DIFFRACTION	100
1.87-1.93	0.1865	143	0.166	1286	X-RAY DIFFRACTION	100
1.93-2	0.1749	140	0.1584	1261	X-RAY DIFFRACTION	100
2-2.08	0.163	143	0.1603	1279	X-RAY DIFFRACTION	100
2.08-2.17	0.1682	142	0.1525	1285	X-RAY DIFFRACTION	100
2.17-2.28	0.1736	143	0.152	1291	X-RAY DIFFRACTION	100
2.28-2.43	0.1761	143	0.1647	1288	X-RAY DIFFRACTION	100
2.43-2.62	0.1753	145	0.162	1300	X-RAY DIFFRACTION	100
2.62-2.88	0.2057	145	0.1703	1311	X-RAY DIFFRACTION	100
2.88-3.29	0.1849	146	0.1709	1308	X-RAY DIFFRACTION	100
3.3-4.15	0.1531	149	0.1424	1341	X-RAY DIFFRACTION	100
4.15-40.33	0.1905	158	0.161	1420	X-RAY DIFFRACTION	100

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	0.3173	0.399	-0.0925	0.4215	0.1912	0.3899	-0.0126	0.0833	-0.0112	-0.0776	0.0279	0.0102	-0.0543	0.0392	-0	0.1309	0.0052	-0.0171	0.1186	-0.0032	0.1307	-21.8005	4.4921	-5.4881
2	0.0586	0.0755	0.0327	0.213	0.1579	-0.0651	0.0481	0.1242	-0.0914	-0.1567	-0.0459	-0.0376	-0.0517	-0.0121	-0.0001	0.1348	-0.0037	-0.0176	0.1411	-0.0217	0.1525	-20.5134	-8.6534	-5.3307
3	0.2157	0.2826	-0.0246	0.2906	-0.0176	0.2111	0.0225	0.1881	-0.0047	0.0247	-0.0222	-0.0581	-0.115	-0.0103	0.0002	0.1386	0.0105	-0.0045	0.1588	-0.0242	0.1421	-29.1366	2.8378	-9.0604
4	0.0733	0.1426	-0.1543	0.0318	-0.1203	0.2343	0.0266	0.096	0.1294	-0.0252	0.0247	0.0432	-0.104	0.0345	0	0.1503	-0.0183	0.0149	0.1647	0.0172	0.1567	-8.6973	8.8674	-8.4089
5	0.7816	0.3503	-0.143	0.384	0.3111	0.4341	0.1293	-0.0314	0.0363	0.1519	-0.0662	-0.0619	-0.0396	0.154	0.1193	0.1712	-0.0117	-0.0287	0.13	-0.0087	0.1163	-14.6237	2.4939	6.7774
6	0.2801	-0.0955	-0.0309	0.2778	-0.2501	0.1903	0.1967	-0.2509	0.1625	0.4309	-0.0606	-0.206	-0.3493	0.1607	0.0394	0.2066	-0.0395	0.0312	0.1543	-0.0251	0.1787	-10.8599	12.4207	2.2979
7	0.4485	-0.2046	-0.1428	0.1441	0.2589	0.3194	0.1143	-0.1305	0.143	-0.0632	-0.0818	-0.3797	-0.1746	0.1276	-0.0024	0.2012	-0.0161	0.0209	0.1395	-0.0273	0.1746	-19.3338	11.8	3.516
8	1.4188	0.1672	0.0459	0.0366	0.0797	0.7779	0.0518	-0.3985	-0.7169	0.7017	-0.034	-0.0913	0.3028	0.0198	-0.0253	0.3546	-0.0388	-0.0468	0.2249	0.1239	0.142	-18.6002	-6.8057	14.8136
9	0.1038	0.0408	0.062	0.2779	-0.1062	0.0804	-0.0294	-0.4334	0.2139	0.3276	0.1736	0.4152	0.0013	0.1208	0.0059	0.2713	-0.006	0.004	0.2342	-0.0326	0.1575	-19.3253	8.438	16.2214
10	0.2592	-0.1156	-0.0095	0.0506	0.0278	0.151	-0.064	-0.1047	-0.1429	0.2453	0.0828	0.112	0.0684	-0.1035	-0.0048	0.1871	-0.0233	0.0204	0.1487	-0.0042	0.1776	-25.5736	-1.4978	7.5367
11	0.2315	-0.148	-0.1404	0.1084	0.1096	0.2979	0.0841	-0.0143	0.1599	0.0712	0.1087	-0.0959	-0.073	0.0245	0.0137	0.1533	-0.0066	0.0374	0.1399	-0.0067	0.1904	-29.8959	9.4682	-0.4211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 57 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 58 through 74 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 75 through 92 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 93 through 104 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 105 through 116 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 117 through 126 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 127 through 137 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 138 through 151 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 152 through 168 )

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