Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T88752 Target Info
Target Name Ras-related C3 botulinum toxin substrate 1 (RAC1)
Synonyms Cell migration-inducing gene5 protein
Target Type Literature-reported Target
Gene Name RAC1
Biochemical Class Small GTPase
UniProt ID
RAC1_HUMAN
Ligand General Information  Top
Ligand Name Phosphoaminophosphonic acid-guanylate ester Ligand Info
Canonical SMILES C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
InChI 1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKey UQABYHGXWYXDTK-UUOKFMHZSA-N
PubChem Compound ID 135403657
Drug Binding Sites of Target  Top
PDB ID: 1I4T      CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN
Method X-ray diffraction Resolution 2.60 Å Mutation Yes [1]
PDB Sequence
QAIKCVVVGD
11
GAVGKTCLLI
21
SYTTNAFPGE
31
YIPTVFDNYS
41
ANVMVDGKPV
51

NLGLWDTAGL
61
EDYDRLRPLS
71
YPQTDVFLIC
81
FSLVSPASFE
91
NVRAKWYPEV
101

RHHCPNTPII
111
LVGTKLDLRD
121
DKDTIEKLKE
131
KKLTPITYPQ
141
GLAMAKEIGA
151

VKYLECSALT
161
QRGLKTVFDE
171
AIRAVLC
Residue
Distance (Å)
GLY10
4.710
ASP11
4.152
GLY12
3.331
ALA13
2.973
VAL14
3.285
GLY15
2.958
LYS16
2.811
THR17
3.029
CYS18
3.223
PHE28
2.984
THR58
4.101
Residue
Distance (Å)
ALA59
3.908
GLY60
3.037
LEU61
4.617
LYS116
3.004
ASP118
3.136
LEU119
2.990
CYS157
4.916
SER158
3.705
ALA159
3.110
LEU160
3.765
PDB ID: 7USE      Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site
Method Electron microscopy Resolution 3.00 Å Mutation Yes [2]
PDB Sequence
QAIKCVVVGD
11
GAVGKTCLLI
21
SYTTNAFSGE
31
YIPTVFDNYS
41
ANVMVDGKPV
51

NLGLWDTAGQ
61
EDYDRLRPLS
71
YPQTDVFLIC
81
FSLVSPASFE
91
NVRAKWYPEV
101

RHHCPNTPII
111
LVGTKLDLRD
121
DKDTIEKLKE
131
KKLTPITYPQ
141
GLAMAKEIGA
151

VKYLECSALT
161
QRGLKTVFDE
171
AIRAVL
Residue
Distance (Å)
ASP11
3.648
GLY12
3.506
ALA13
3.474
VAL14
3.520
GLY15
3.236
LYS16
3.039
THR17
2.741
CYS18
3.109
PHE28
3.505
SER29
3.003
GLY30
3.174
GLU31
3.466
TYR32
3.730
ILE33
4.582
Residue
Distance (Å)
PRO34
3.435
THR35
2.857
ASP57
4.617
THR58
3.631
ALA59
3.955
GLY60
3.566
GLN61
4.388
THR115
4.514
LYS116
3.447
ASP118
3.419
LEU119
3.395
SER158
4.127
ALA159
3.355
LEU160
3.868
PDB ID: 3SBD      Crystal structure of RAC1 P29S mutant
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [3]
PDB Sequence
GQAIKCVVVG
10
DGAVGKTCLL
20
ISYTTNAFSG
30
EYIPTVFDNY
40
SANVMVDGKP
50

VNLGLWDTAG
60
QEDYDRLRPL
70
SYPQTDVFLI
80
CFSLVSPASF
90
ENVRAKWYPE
100

VRHHCPNTPI
110
ILVGTKLDLR
120
DDKDTIEKLK
130
EKKLTPITYP
140
QGLAMAKEIG
150

AVKYLECSAL
160
TQRGLKTVFD
170
EAIRAVL
Residue
Distance (Å)
GLY10
4.626
ASP11
3.863
GLY12
3.602
ALA13
3.076
VAL14
3.415
GLY15
3.124
LYS16
2.712
THR17
2.951
CYS18
2.875
LEU19
4.923
PHE28
3.517
SER29
2.889
GLY30
2.853
GLU31
3.942
TYR32
2.432
Residue
Distance (Å)
ILE33
4.370
PRO34
3.727
THR35
2.929
ASP57
4.770
THR58
4.181
ALA59
3.984
GLY60
2.807
GLN61
4.325
LYS116
3.214
ASP118
2.941
LEU119
3.552
CYS157
4.920
SER158
3.475
ALA159
2.992
LEU160
3.515
PDB ID: 3SBE      Crystal structure of RAC1 P29S mutant
Method X-ray diffraction Resolution 2.60 Å Mutation Yes [3]
PDB Sequence
QGQAIKCVVV
9
GDGAVGKTCL
19
LISYTTNAFS
29
GEYIPTVFDN
39
YSANVMVDGK
49

PVNLGLWDTA
59
GQEDYDRLRP
69
LSYPQTDVFL
79
ICFSLVSPAS
89
FENVRAKWYP
99

EVRHHCPNTP
109
IILVGTKLDL
119
RDDKDTIEKL
129
KEKKLTPITY
139
PQGLAMAKEI
149

GAVKYLECSA
159
LTQRGLKTVF
169
DEAIRAVL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:116 or .A:118 or .A:119 or .A:158 or .A:159 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.505
ASP11
3.536
GLY12
3.673
ALA13
3.328
VAL14
3.064
GLY15
3.120
LYS16
2.656
THR17
2.658
CYS18
2.833
LEU19
4.942
PHE28
3.305
SER29
2.630
GLY30
2.833
GLU31
4.180
TYR32
2.622
Residue
Distance (Å)
ILE33
4.427
PRO34
3.909
THR35
2.709
ASP57
4.466
THR58
4.157
ALA59
4.076
GLY60
2.930
GLN61
4.471
LYS116
3.225
ASP118
2.688
LEU119
3.153
SER158
3.259
ALA159
2.781
LEU160
3.265
PDB ID: 1MH1      SMALL G-PROTEIN
Method X-ray diffraction Resolution 1.38 Å Mutation Yes [4]
PDB Sequence
GSPQAIKCVV
8
VGDGAVGKTC
18
LLISYTTNAF
28
PGEYIPTVFD
38
NYSANVMVDG
48

KPVNLGLWDT
58
AGQEDYDRLR
68
PLSYPQTDVS
78
LICFSLVSPA
88
SFENVRAKWY
98

PEVRHHCPNT
108
PIILVGTKLD
118
LRDDKDTIEK
128
LKEKKLTPIT
138
YPQGLAMAKE
148

IGAVKYLECS
158
ALTQRGLKTV
168
FDEAIRAVLC
178
PPP
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:116 or .A:118 or .A:119 or .A:158 or .A:159 or .A:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.611
ASP11
3.876
GLY12
3.444
ALA13
3.074
VAL14
3.301
GLY15
2.978
LYS16
2.658
THR17
2.945
CYS18
2.802
LEU19
4.924
PHE28
3.383
GLU31
3.027
TYR32
3.234
ILE33
3.949
Residue
Distance (Å)
PRO34
3.554
THR35
3.296
ASP57
4.894
THR58
4.125
ALA59
3.819
GLY60
2.803
GLN61
4.262
LYS116
3.125
ASP118
2.759
LEU119
3.463
SER158
3.485
ALA159
2.976
LEU160
3.301
PDB ID: 3SU8      Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1
Method X-ray diffraction Resolution 3.20 Å Mutation No [5]
PDB Sequence
MQAIKCVVVG
10
DGAVGKTCLL
20
ISYTTNAFPG
30
EYIPTVFDNY
40
SANVMVDGKP
50

VNLGLWDTAG
60
QEDYDRLRPL
70
SYPQTDVFLI
80
CFSLVSPASF
90
ENVRAKWYPE
100

VRHHCPNTPI
110
ILVGTKLDLR
120
DDKDTIEKLK
130
EKKLTPITYP
140
QGLAMAKEIG
150

AVKYLECSAL
160
TQRGLKTVFD
170
EAIRAVLK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:30 or .A:32 or .A:33 or .A:34 or .A:35 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:116 or .A:118 or .A:119 or .A:157 or .A:158 or .A:159 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.714
ASP11
3.483
GLY12
3.380
ALA13
3.386
VAL14
3.263
GLY15
3.005
LYS16
2.791
THR17
2.712
CYS18
2.852
LEU19
4.977
PHE28
3.308
GLY30
3.221
TYR32
3.262
ILE33
4.441
Residue
Distance (Å)
PRO34
3.583
THR35
3.008
ASP57
4.417
THR58
3.370
ALA59
4.216
GLY60
3.227
GLN61
2.769
LYS116
3.343
ASP118
2.973
LEU119
3.430
CYS157
4.992
SER158
3.604
ALA159
2.760
LEU160
3.627
PDB ID: 3SUA      Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1
Method X-ray diffraction Resolution 4.39 Å Mutation No [5]
PDB Sequence
MQAIKCVVVG
10
DGAVGKTCLL
20
ISYTTNAFPG
30
EYIPTVFDNY
40
SANVMVDGKP
50

VNLGLWDTAG
60
QEDYDRLRPL
70
SYPQTDVFLI
80
CFSLVSPASF
90
ENVRAKWYPE
100

VRHHCPNTPI
110
ILVGTKLDLR
120
DDKDTIEKLK
130
EKKLTPITYP
140
QGLAMAKEIG
150

AVKYLECSAL
160
TQRGLKTVFD
170
EAIRAVLK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:28 or .A:30 or .A:32 or .A:33 or .A:34 or .A:35 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:158 or .A:159 or .A:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.263
ASP11
3.690
GLY12
3.477
ALA13
3.327
VAL14
3.132
GLY15
3.011
LYS16
2.864
THR17
2.517
CYS18
2.902
PHE28
3.345
GLY30
3.554
TYR32
2.683
ILE33
4.044
PRO34
3.418
Residue
Distance (Å)
THR35
2.965
ASP57
4.279
THR58
3.138
ALA59
4.122
GLY60
3.226
GLN61
2.767
THR115
3.837
LYS116
3.411
LEU117
4.897
ASP118
2.725
LEU119
3.399
SER158
2.962
ALA159
2.683
LEU160
3.486
PDB ID: 1RYH      Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
Method X-ray diffraction Resolution 1.75 Å Mutation No [6]
PDB Sequence
GSMQAIKCVV
8
VGDGAVGKTC
18
LLISYTTNAF
28
PGEYIPTVFD
38
NYSANVMVDG
48

KPVNLGLWDT
58
AGIADVFLIC
100
FSLVSPASFE
110
NVRAKWYPEV
120
RHHCPNTPII
130

LVGTKLDLRD
140
DKDTIEKLKE
150
KKLTPITYPQ
160
GLAMAKEIGA
170
VKYLECSALT
180

QRGLKTVFDE
190
AIRAVLCPPP
200
V
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:57 or .A:58 or .A:59 or .A:60 or .A:135 or .A:137 or .A:138 or .A:176 or .A:177 or .A:178 or .A:179; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.842
ASP11
3.913
GLY12
3.403
ALA13
3.194
VAL14
3.421
GLY15
3.055
LYS16
2.679
THR17
2.972
CYS18
2.841
LEU19
4.913
PHE28
3.457
Residue
Distance (Å)
ASP57
4.904
THR58
4.096
ALA59
4.321
GLY60
3.316
LYS135
3.151
ASP137
2.855
LEU138
3.563
CYS176
4.969
SER177
3.417
ALA178
2.903
LEU179
3.291
PDB ID: 4GZL      Crystal structure of RAC1 Q61L mutant
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [7]
PDB Sequence
AIKCVVVGDG
12
AVGKTCLLIS
22
YTTNAFPGYI
33
PTVFDNYSAN
43
VMVDKPVNLG
54

LWDTAGLEDY
64
DRLRPLSYPQ
74
TDVFLICFSL
84
VSPASFENVR
94
AKWYPEVRHH
104

CPNTPIILVG
114
TKLDLRDDKD
124
TIEKLKEKKL
134
TPITYPQGLA
144
MAKEIGAVKY
154

LECSALTQRG
164
LKTVFDEAIR
174
AVL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:29 or .A:32 or .A:33 or .A:34 or .A:35 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:116 or .A:118 or .A:119 or .A:158 or .A:159 or .A:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.629
ASP11
3.828
GLY12
3.558
ALA13
2.745
VAL14
3.300
GLY15
3.054
LYS16
2.616
THR17
2.862
CYS18
2.730
LEU19
4.876
PHE28
3.372
PRO29
4.482
TYR32
2.422
ILE33
4.483
Residue
Distance (Å)
PRO34
3.465
THR35
2.731
ASP57
4.566
THR58
4.004
ALA59
3.862
GLY60
2.710
LEU61
4.286
LYS116
3.006
ASP118
2.779
LEU119
3.391
SER158
3.559
ALA159
3.042
LEU160
3.206
PDB ID: 3TH5      Crystal structure of wild-type RAC1
Method X-ray diffraction Resolution 2.30 Å Mutation No [3]
PDB Sequence
QAIKCVVVGD
11
GAVGKTCLLI
21
SYTTNAFPGE
31
YIPTVFDNYS
41
ANVMVDGKPV
51

NLGLWDTAGQ
61
EDYDRLRPLS
71
YPQTDVFLIC
81
FSLVSPASFE
91
NVRAKWYPEV
101

RHHCPNTPII
111
LVGTKLDLRD
121
DKDTIEKLKE
131
KKLTPITYPQ
141
GLAMAKEIGA
151

VKYLECSALT
161
QRGLKTVFDE
171
AIRAVL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:28 or .A:32 or .A:33 or .A:34 or .A:35 or .A:58 or .A:59 or .A:60 or .A:61 or .A:116 or .A:118 or .A:119 or .A:157 or .A:158 or .A:159 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.701
ASP11
3.793
GLY12
3.318
ALA13
2.998
VAL14
3.309
GLY15
3.095
LYS16
2.647
THR17
3.094
CYS18
2.879
LEU19
4.838
PHE28
3.300
TYR32
3.266
ILE33
4.617
Residue
Distance (Å)
PRO34
3.779
THR35
2.730
THR58
4.435
ALA59
4.279
GLY60
3.132
GLN61
4.540
LYS116
3.359
ASP118
2.921
LEU119
3.291
CYS157
4.994
SER158
3.661
ALA159
2.828
LEU160
3.242
PDB ID: 3RYT      The Plexin A1 intracellular region in complex with Rac1
Method X-ray diffraction Resolution 3.58 Å Mutation Yes [8]
PDB Sequence
QAIKCVVVGD
11
GAVGKTCLLI
21
SYTTNAFPGE
31
YIPTVFDNYS
41
ANVMVDGKPV
51

NLGLWDTAGE
62
DYDRLRPLSY
72
PQTDVFLICF
82
SLVSPASFEN
92
VRAKWYPEVR
102

HHCPNTPIIL
112
VGTKLDLRDD
122
KDTIEKLKEK
132
KLTPITYPQG
142
LAMAKEIGAV
152

KYLECSALTQ
162
RGLKTVFDEA
172
IRAV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GNP or .GNP2 or .GNP3 or :3GNP;style chemicals stick;color identity;select .C:10 or .C:11 or .C:12 or .C:13 or .C:14 or .C:15 or .C:16 or .C:17 or .C:18 or .C:19 or .C:28 or .C:30 or .C:31 or .C:32 or .C:33 or .C:34 or .C:35 or .C:57 or .C:58 or .C:59 or .C:60 or .C:115 or .C:116 or .C:117 or .C:118 or .C:158 or .C:159 or .C:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY10
4.650
ASP11
3.972
GLY12
3.513
ALA13
2.811
VAL14
3.309
GLY15
3.027
LYS16
2.764
THR17
2.707
CYS18
2.922
LEU19
4.798
PHE28
3.439
GLY30
3.539
GLU31
4.549
TYR32
2.944
Residue
Distance (Å)
ILE33
4.320
PRO34
3.528
THR35
2.782
ASP57
4.925
THR58
4.083
ALA59
4.012
GLY60
3.990
THR115
4.857
LYS116
3.369
LEU117
4.631
ASP118
2.780
SER158
3.296
ALA159
2.756
LEU160
3.266
References  Top
REF 1 The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Nature. 2001 May 10;411(6834):215-9.
REF 2 Structures reveal a key mechanism of WAVE regulatory complex activation by Rac1 GTPase. Nat Commun. 2022 Sep 16;13(1):5444.
REF 3 Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet. 2012 Sep;44(9):1006-14.
REF 4 The crystal structure of human rac1, a member of the rho-family complexed with a GTP analogue. Nat Struct Biol. 1997 Feb;4(2):147-52.
REF 5 A dual binding mode for RhoGTPases in plexin signalling. PLoS Biol. 2011 Aug;9(8):e1001134.
REF 6 Alternative splicing of Rac1 generates Rac1b, a self-activating GTPase. J Biol Chem. 2004 Feb 6;279(6):4743-9.
REF 7 RAC1P29S is a spontaneously activating cancer-associated GTPase. Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):912-7.
REF 8 Plexins are GTPase-activating proteins for Rap and are activated by induced dimerization. Sci Signal. 2012 Jan 17;5(207):ra6.

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