Table 1.

GEF:Small GTPase structures.

No	PDB ID	Year	GEF	SmallG	GEF	Reso	Ligand *1	Disorder *2 (p,sw1,sw2)	HVR *3
1	1LFD	1998	RALGDS	H-Ras	RasGEF	2.1	GNP	no, no, no	no
2	1BKD	1998	SOS1	H-Ras	RasGEF	2.8		no, no, no	no
3	1NVU	2000	SOS1	H-Ras	RasGEF	2.2		no, no, no	no
4	1NVV	2003	SOS1	H-Ras	RasGEF	2.2	GNP	no, no, no	no
5	1NVW	2003	SOS1	H-Ras	RasGEF	2.7	GNP	no, no, no	no
6	1NVX	2003	SOS1	H-Ras	RasGEF	3.2	GTP	no, no, no	no
7	1XD2	2004	SOS1	H-Ras	RasGEF	2.7	GDP	no, no, no	no
8	3CF6	2008	Epac2	Rap1B	RapGEF	2.2	SO4	no, no, no	no
9	4NYJ	2014	SOS1	H-Ras	RasGEF	2.9	GNP	no, no, no	no
10	4NYM	2014	SOS1	H-Ras	RasGEF	3.6		no, no, no	no
11	4MGI	2014	Epac	Rap1b	RapGEF	2.8	SO4	no, no, no	no
12	4MGK	2014	Epac	Rap1b	RapGEF	2.7	SO4	no, no, no	no
13	4MGY	2014	Epac	Rap1b	RapGEF	2.6	SO4	no, no, no	no
14	4MGZ	2014	Epac	Rap1b	RapGEF	3.0	SO4	no, no, no	no
15	4MH0	2014	Epac	Rap1b	RapGEF	2.4	SO4	no, no, no	no
16	4URU	2015	SOS1	H-Ras	RasGEF	2.8		no, no, no	no
17	4URV	2015	SOS1	H-Ras	RasGEF	2.6		no, no, no	no
18	4URW	2015	SOS1	H-Ras	RasGEF	2.8		no, no, no	no
19	4URX	2015	SOS1	H-Ras	RasGEF	2.5		no, no, no	no
20	4URY	2015	SOS1	H-Ras	RasGEF	2.5		no, no, no	no
21	4URZ	2015	SOS1	H-Ras	RasGEF	2.2		no, no, no	no
22	4US0	2015	SOS1	H-Ras	RasGEF	2.2		no, no, no	no
23	4US1	2015	SOS1	H-Ras	RasGEF	2.7	L71	no, no, no	no
24	4US2	2015	SOS1	H-Ras	RasGEF	2.5	L71	no, no, no	no
25	5CM8	2015	Rlf (Rgl2)	RalA	RalGEF	2.6		no, no, no	no
26	6AXG	2017	RasGRP4	H-Ras	RasGEF	3.3		no, yes, no	no
27	6AXF	2017	RasGRP	Rap1b	RapGEF	3.1		no, no, no	no
28	6D55	2018	SOS1	H-Ras	RasGEF	1.7	Na, FMT, GOL, Mg, GNP, FWA	no, no, no	no
29	6D5W	2018	SOS1	H-Ras	RasGEF	2.5	FVV, Mg, GNP	no, no, no	no
30	6D56	2018	SOS1	H-Ras	RasGEF	1.7	Na, FMT, GOL, Mg, GNP, FVN	no, no, no	no
31	6D59	2018	SOS1	H-Ras	RasGEF	1.7	Na, FMT, GOL, Mg, GNP, FVJ	no, no, no	no
32	6D5E	2018	SOS1	H-Ras	RasGEF	1.8	Na, FMT, GOL, Mg, GNP, FVG, CL	no, no, no	no
33	6D5G	2018	SOS1	H-Ras	RasGEF	1.9	FMT, GOL, Mg, GNP, FVD, Cl, BME	no, no, no	no
34	6D5H	2018	SOS1	H-Ras	RasGEF	1.8	FMT, GOL, MG, GNP, FV7, Cl	no, no, no	no
35	6D5J	2018	SOS1	H-Ras	RasGEF	1.8	Na, FMT, GOL, MG, GNP, FV4	no, no, no	no
36	6D5L	2018	SOS1	H-Ras	RasGEF	1.7	Na, FMT, GOL, MG, GNP, FW7	no, no, no	no
37	6D5V	2018	SOS1	H-Ras	RasGEF	2.0	Mg, GNP, FVY	no, no, no	no
38	6D5M	2018	SOS1	H-Ras	RasGEF	2.1	Mg, GNP, FW4	no, no, no	no
39	5WFO	2018	SOS1	H-Ras	RasGEF	2.0	Mg, GNP, 5UU	no, no, no	no
40	5WFP	2018	SOS1	H-Ras	RasGEF	2.1	Mg, GNP, 5UX	no, no, no	no
41	5WFQ	2018	SOS1	H-Ras	RasGEF	2.3	Mg, GNP, 5UV	no, no, no	no
42	5WFR	2018	SOS1	H-Ras	RasGEF	2.5	Mg, GNP, 5UW	no, no, no	no
43	6BVI	2018	SOS1	H-Ras	RasGEF	1.8	NA, FMT, EC4, GOL, Mg, GNP	no, no, no	no
44	6BVJ	2018	SOS1	H-Ras	RasGEF	1.7	NA, FMT, EAS, GOL, Mg, GNP	no, no, no	no
45	6BVK	2018	SOS1	H-Ras	RasGEF	1.8	NA, FMT, EAV, GOL, Mg, GNP	no, no, no	no
46	6BVL	2018	SOS1	H-Ras	RasGEF	1.7	NA, FBY, EAV, GOL, Mg, GNP	no, no, no	no
47	6BVM	2018	SOS1	H-Ras	RasGEF	1.8	NA, FBY, EBV, GOL, Mg, GNP	no, no, no	no
48	6EPL	2019	SOS1	K-Ras	RasGEF	2.6	GOL	no, no, no	no
49	6EPM	2019	SOS1	K-Ras	RasGEF	2.5	BQ5, GOL	no, no, no	no
50	6EPN	2019	SOS1	K-Ras	RasGEF	2.5	BQ2, DMS, GOL	no, no, no	no
51	6EPO	2019	SOS1	K-Ras	RasGEF	2.4	GOL, BPW	no, no, no	no
52	6EPP	2019	SOS1	K-Ras	RasGEF	2.4	GOL, BOQ	no, no, no	no
53	1LB1	2002	Dbs (Mcf21)	RhoA	RhoGEF	2.8		no, no, no	no
54	1 × 86	2004	ARHGEF12	RhoA	RhoGEF	3.2	PO4	no, no, no	no
55	1XCG	2004	ARHGEF11 (PDZ-rhoGEF)	RhoA	RhoGEF	2.5		no, no, no	no
56	2RGN	2007	ARHGEF25 (p63RhoGEF)	RhoA	RhoGEF	3.5		no, no, no	no
57	3KZ1	2010	ARHGEF11 (PDZ-rhoGEF)	RhoA	RhoGEF	2.7	GSP	no, no, no	no
58	3LW8	2010	IpgB2	RhoA	RhoGEF	1.9	GDP	no, no, no	no
59	3LWN	2010	IpgB2	RhoA	RhoGEF	2.3	GDP	no, no, no	no
60	3LXR	2010	IpgB2	RhoA	RhoGEF	1.7	GDP	no, no, no	no
61	3T06	2011	ARHGEF11 (PDZ-rhoGEF)	RhoA	RhoGEF	2.8		no, no, no	no
62	4D0N	2014	AKAP13	RhoA	RhoGEF	2.1	GDP	no, no, no	no
63	4XH9	2015	NET1 (ARHGEF8)	RhoA	RhoGEF	2.0		no, yes, no	no
64	6BC0	2017	ARHGEF28 (p190RhoGEF)	RhoA	RhoGEF	2.2	GSP	no, no, no	no
65	5JHG	2017	ARHGEF11	RhoA	RhoGEF	2.5	GOL	no, no, no	no
66	6BCA	2017	ARHGEF18 (LbcRhoGEF)	RhoA	RhoGEF	2.0	GSP	no, no, no	no
67	6BCB	2017	ARHGEF18 (p114RhoGEF)	RhoA	RhoGEF	1.4	GSP	no, no, no	no
68	5JHH	2017	ARHGEF11	RhoA	RhoGEF	2.3	RAO	no, no, no	no
69	5ZHX	2018	SmgGDS	RhoA	RhoGEF	3.5		yes, yes, yes	yes
70	1FOE	2000	Tiam	Rac1	RhoGEF	2.8	SO4	no, no, no	no
71	2NZ8	2007	Trio	Rac1	RhoGEF	2.0		no, no, no	no
72	2VRW	2008	Vav1	Rac1	RhoGEF	1.9		no, no, no	no
73	2YIN	2011	DOCK2	Rac1	RhoGEF	2.7		no, no, no	no
74	3B13	2012	DOCK2	Rac1	RhoGEF	3.0		no, no, no	no
75	3BJI	2007	Vav1	Rac1	RhoGEF	2.6		no, no, no	no
76	4YON	2015	P-Rex1	Rac1	RhoGEF	2.0		no, no, no	no
77	5FI0	2016	P-Rex1	Rac1	RhoGEF	3.3		no, no, no	yes
78	5O33	2017	Kalirin	Rac1	RhoGEF	1.6	GDP	no, no, no	no
79	6BC1	2018	ARHGEF28 (p190RhoGEF)	Rac1	RhoGEF	2.9	GSP	no, no, no	no
80	1KZ7	2002	Dbs (Mcf2l)	Cdc42	RhoGEF	2.4		no, no, no	no
81	1GZS	2002	SOPE	Cdc42	RhoGEF	2.3	PO4	no, no, no	no
82	1KI1	2002	ITSN1	Cdc42	RhoGEF	2.3	PO4	no, no, no	no
83	1KZG	2002	Mcf2l (Dbs)	Cdc42	RhoGEF	2.6		no, no, no	no
84	2DFK	2006	ARHGEF9 (Collybistin II)	Cdc42	RhoGEF	2.2	PO4	no, no, no	yes
85	2WM9	2009	DOCK9	Cdc42	RhoGEF	2.2	GOL	no, no, no	no
86	2WMN	2009	DOCK9	Cdc42	RhoGEF	2.4	GDP	no, no, no	no
87	2WMO	2009	DOCK9	Cdc42	RhoGEF	2.2	GDP	no, no, no	no
88	3GCG	2009	map (L0028)	Cdc42	RhoGEF	2.3		no, yes, no	no
89	3QBV	2012	ITSN1	Cdc42	RhoGEF	2.7	GDP	no, yes, no	no
90	3VHL	2012	DOCK8	Cdc42	RhoGEF	2.1	PO4	no, no, no	no
91	6AJ4	2019	DOCK7	Cdc42	RhoGEF	3.2		no, no, no	yes
92	6AJL	2019	DOCK7	Cdc42	RhoGEF	3.2		no, no, no	yes
93	3CX6	2008	ARHGEF11 (PDZRhoGEF)	Galpha-13	RhoGEF	2.5	GDP	no, no, no	no
94	3CX7	2008	ARHGEF11 (PDZRhoGEF)	Galpha-13	RhoGEF	2.3	GSP	no, no, no	no
95	3CX8	2008	ARHGEF11 (PDZRhoGEF)	Galpha-13	RhoGEF	2.5	GDP	no, no, no	no
96	1SHZ	2005	ARHGEF1 (p115RhoGEF)	Gnai1,13	RhoGEF	2.9	GDP+ALF	no, no, no	no
97	2NTY	2007	ROPGEF8	ROP4	RopGEF	3.1	GDP	no, yes, no	no
98	2WBL	2009	ROPGEF8	ROP7	RopGEF	2.9		no, yes, no	no
99	2WWX	2009	SidM/DrrA	Rab1	RabGEF	1.5		no, no, no	no
100	3L0I	2010	SidM/DrrA	Rab1	RabGEF	2.9	SO4	no, no, no	no
101	3JZA	2010	DrrA/SidM	Rab1b	RabGEF	1.8	PO4	no, no, no	no
102	5O74	2017	DrrA/SidM	Rab1b	RabGEF	2.5	GDP	no, yes, yes	no
103	2OT3	2007	Rabex-5 (RabGEF1)	Rab21	RabGEF	2.1		no, yes, no	no
104	3TW8	2011	DENND1B	Rab35	RabGEF	2.1		no, yes, no	no
105	4Q9U	2014	Rabex-5 (RabGEF1)	Rab5A	RabGEF	4.6		yes, yes, no	no
106	2FU5	2006	MSS4	Rab8A	RabGEF	2.0		no, yes, yes	no
107	4LHX	2013	RAB3IP (Rabin8)	Rab8A	RabGEF	3.1	SO4	no, no, no	no
108	4LHY	2013	RAB3IP (Rabin8)	Rab8A	RabGEF	3.1	GDP	no, no, no	no
109	4LHZ	2013	RAB3IP (Rabin8)	Rab8A	RabGEF	3.2	GTP	no, no, no	no
110	4LI0	2013	RAB3IP (Rabin8)	Rab8A	RabGEF	3.3	GDP	no, no, no	no
111	2EFD	2010	AtVps9a	Ara7 (RabF2B)	RabGEF	3.0		no, yes, no	no
112	2EFE	2010	AtVps9a	Ara7 (RabF2B)	RabGEF	2.1	GDP	no, no, no	no
113	2EFH	2010	AtVps9a	Ara7 (RabF2B)	RabGEF	2.1	GDP	no, yes, no	no
114	2EFC	2010	AtVps9a	Ara7 (RabF2B)	RabGEF	2.1	GDP	no, no, no	no
115	4G01	2013	Vps9a	Ara7 (RabF2B)	RabGEF	2.2	GDP	no, no, no	no
116	2OCY	2007	Sec2p	Sec4p	RabGEF	3.3	GDP	no, no, no	no
117	2EQB	2007	Sec2p	Sec4p	RabGEF	2.7		no, no, no	no
118	4ZDW	2015	Sec2p	Sec4p	RabGEF	2.9		no, no, no	no
119	3CUE	2008	TRAPPI assembly	Ypt1p	RabGEF	3.7		no, yes, no	no
120	5LDD	2017	Mon1-Ccz1	Ypt7	RabGEF	2.5	SO4	no, no, no	no
121	6IXV	2019	SH3BP5	Rab11	RabGEF	3.8	PO4	no, no, no	no
122	6EKK	2019	DENND 1A	Rab35	RabGEF	1.8	GDP, SO4, EDO	no, no, no	no
123	6DJL	2019	SH3BP5	Rab11	RabGEF	3.1		no, no, no	no
124	1RE0	2003	GEA1	ARF1	ArfGEF	2.4	GDP	no, no, no	no
125	1R8Q	2003	CYTH2 (Arno)	ARF1	ArfGEF	1.9	G3D	no, no, no	no
126	1R8S	2003	CYTH2 (Arno)	ARF1	ArfGEF	1.5	GDP	no, no, no	no
127	1S9D	2003	CYTH2 (Arno)	ARF1	ArfGEF	1.8	GDP	no, yes, no	no
128	4C0A	2013	IQSEC1	ARF1	ArfGEF	3.3	G3D	no, no, no	no
129	6FAE	2018	IQSEC2	ARF1	ArfGEF	2.3		no, yes, no	no
130	4KAX	2013	CYTH3	ARF6	ArfGEF	1.9	GTP	no, no, no	no
131	5EE5	2016	ARFGEF1	ARL1	ArfGEF	2.3	GTP	no, no, no	no
132	5J5C	2016	ARFGEF1	ARL1	ArfGEF	3.4	GTP	no, no, no	no
133	1I2M	2001	RCC1	RAN	RanGEF	1.8	SO4	no, yes, no	no

*1 The names of the ligands are described below. GNP: phosphoaminophosphonic acid-guanylate ester; L71: (3S)-3-[3-(aminomethyl)phenyl]-1-ethylpyrrolidine-2,5-dione; FMT: formic acid; GOL: glycerol; FWA: 6-chloro-2-(2,6-diazaspiro [3.3]heptan-2-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-4-(4-methylpiperazin-1-yl)-1H-benzimidazole; FVV: 10-[(4-fluorophenyl)methyl]-2,3,4,10-tetrahydropyrimido [1,2-a]benzimidazole; FVN: 6-chloro-2-(2,6-diazaspiro[3.3]heptan-2-yl)-4-(3,5-dimethyl-1H-pyrazol-4-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-1H-benzimidazole; FVJ: 6-chloro-4-(3,5-dimethyl-1H-pyrazol-4-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole; FVG: 1-[(2S)-1-{6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazol-4-yl}pyrrolidin-2-yl]methanamine; FVD: 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole; BME: beta-mercaptoethanol; FV7: 6-chloro-4-(2-chlorophenyl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole; FV4: 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole; FW7: 6-chloro-1-[(3-chloro-4-fluorophenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole; FVY: 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-1H-benzimidazol-2-amine; FW4: 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-2-(piperazin-1-yl)-1H-benzimidazole; 5UU: 6-chloranyl-~{N}-(4-fluorophenyl)-1,2,3,4-tetrahydroacridin-9-amine; 5UX: 6-chloranyl-~{N}-(3-chloranyl-4-fluoranyl-phenyl)-1,2,3,4-tetrahydroacridin-9-amine; 5UV: 7-chloranyl-~{N}-(3-chloranyl-4-fluoranyl-phenyl)-1,2,3,4-tetrahydroacridin-9-amine; 5UW: ~{N}-(3,3-diphenylpropyl)piperidin-4-amine; EC4: 6-chloro-N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide; EAS: 5-chloro-N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide; EAV: N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-6-methyl-L-tryptophanamide; EBY: N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-5-methyl-L-tryptophanamide; EBV: (2S)-2-amino-1-[(3aR,6aS)-5-[(5-chloro-1H-indol-3-yl)methyl]hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-3-(1H-indol-3-yl)propan-1-one; BQ5: (1-phenyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)methanamine; BQ2: 1-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-ethanone, DMS: dimethyl sulfoxide; BPW: 3-(4-chlorophenyl)propan-1-amine; BOQ: ethyl 2-(aminomethyl)-5-~{tert}-butyl-furan-3-carboxylate; GSP: 5′-guanosine-diphosphate-monothiophosphate; RA0: 3-{3-[ethyl(quinolin-2-yl)amino]phenyl}propanoic acid; ALF: tetrafluoroaluminate ion; EDO: 1,2-ethanediol; G3D: guanosine-3′-monophosphate-5′-diphosphate. *2 Disordered regions among P-loop (p), switch I (sw1), and switch II (sw2) are indicated. “yes” means that the region has a disordered structure. *3 The structure including the hyper variable region (HVR) is indicated as “yes”.