Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Guanosine-5'-Diphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N | ||||
| InChI | 1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 | ||||
| InChIKey | QGWNDRXFNXRZMB-UUOKFMHZSA-N | ||||
| PubChem Compound ID | 135398619 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1I4D CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [1] |
| PDB Sequence |
QAIKCVVVGD
11 GAVGKTCLLI21 SYTTNAFPGE31 YIPTVFDNYS41 ANVMVDGKPV51 NLGLWDTAGQ 61 EDYDRLRPLS71 YPQTDVFLIC81 FSLVSPASFE91 NVRAKWYPEV101 RHHCPNTPII 111 LVGTKLDLRD121 DKDTIEKLKE131 KKLTPITYPQ141 GLAMAKEIGA151 VKYLECSALT 161 QRGLKTVFDE171 AIRAVLC
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| PDB ID: 1HH4 Rac1-RhoGDI complex involved in NADPH oxidase activation | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [2] |
| PDB Sequence |
PQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 EYIPTVFDNY40 SANVMVDGKP50 VNLGLWDTAG 60 QEDYDRLRPL70 SYPQTDVSLI80 CFSLVSPASF90 ENVRAKWYPE100 VRHHCPNTPI 110 ILVGTKLDLR120 DDKDTIEKLK130 EKKLTPITYP140 QGLAMAKEIG150 AVKYLECSAL 160 TQRGLKTVFD170 EAIRAVLCPP180 PVKKRKRKC
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ASP11
3.789
GLY12
3.512
ALA13
2.595
VAL14
3.289
GLY15
2.900
LYS16
2.943
THR17
2.757
CYS18
2.986
LEU19
4.949
PHE28
3.404
PRO29
4.576
|
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| PDB ID: 1I4L CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41) | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
QAIKCVVVGD
11 GAVGKTCLLI21 SYTTNAFPGE31 YIPTVFDNYS41 ANVMVDGKPV51 NLGLWDTAGQ 61 EDYDRLRPLS71 YPQTDVFLIC81 FSLVSPASFE91 NVRAKWYPEV101 RHHCPNTPII 111 LVGTKLDLRD121 DKDTIEKLKE131 KKLTPITYPQ141 GLAMAKEIGA151 VKYLECSALT 161 QRGLKTVFDE171 AIRAVLC
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| PDB ID: 2P2L Rac1-GDP-Zinc Complex | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [3] |
| PDB Sequence |
MQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 EYIPTVFDNY40 SANVGKPVNL53 GLWDTAGQED 63 YDRLRPLSYP73 QTDVSLICFS83 LVSPASFENV93 RAKWYPEVRH103 HCPNTPIILV 113 GTKLDLRDDK123 DTIEKLKEKK133 LTPITYPQGL143 AMAKEIGAVK153 YLECSALTQR 163 GLKTVFDEAI173 RAVLCP
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:33 or .A:34 or .A:35 or .A:57 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
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| PDB ID: 2H7V Co-crystal structure of YpkA-Rac1 | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | Yes | [4] |
| PDB Sequence |
GSKLMQAIKC
6 VVVGDGAVGK16 TCLLISYTTN26 AFPGEYIPTV36 FDNYSANVMV46 DGKPVNLGLW 56 DTAGQEDYDR66 LRPLSYPQTD76 VSLICFSLVS86 PASFENVRAK96 WYPEVRHHCP 106 NTPIILVGTK116 LDLRDDKDTI126 EKLKEKKLTP136 ITYPQGLAMA146 KEIGAVKYLE 156 CSALTQRGLK166 TVFDEAIRAV176 LC
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:33 or .A:34 or .A:35 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
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| PDB ID: 1G4U CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1 | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [5] |
| PDB Sequence |
MQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 EYIPTVFDNY40 SANVMVDGKP50 VNLGLWDTAG 60 QEDYDRLRPL70 SYPQTDVSLI80 CFSLVSPASF90 ENVRAKWYPE100 VRHHCPNTPI 110 ILVGTKLDLR120 DDKDTIEKLK130 EKKLTPITYP140 QGLAMAKEIG150 AVKYLECSAL 160 TQRGLKTVFD170 EAIRAVLCPP180
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .R:11 or .R:12 or .R:13 or .R:14 or .R:15 or .R:16 or .R:17 or .R:18 or .R:19 or .R:28 or .R:32 or .R:35 or .R:57 or .R:116 or .R:118 or .R:119 or .R:158 or .R:159 or .R:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6AGP Structure of Rac1 in the low-affinity state for Mg2+ | ||||||
| Method | Solution NMR | Resolution | N.A. | Mutation | Yes | [6] |
| PDB Sequence |
MQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 CYIPTVFDNY40 SANVMVDGKP50 VNLGLWDTAG 60 QECYDRLRPL70 SYPCTDVFLI80 CFSLVSPASF90 ENVRAKWYPE100 VRHHCPNTPI 110 ILVGTKLDLR120 DDKDTIEKLK130 EKKLTPITYP140 QGLAMAKEIG150 AVKYLECSAC 160 TQRGLKTVFD170 EAIRAVLCPP180 P
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:158 or .A:159 or .A:160 or .A:161; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 1RYF Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [7] |
| PDB Sequence |
GSMQAIKCVV
8 VGDGAVGKTC18 LLISYTTNAF28 PGEYIPTVFD38 NYSANVMVDG48 KPVNLGLWDT 58 AIADVFLICF101 SLVSPASFEN111 VRAKWYPEVR121 HHCPNTPIIL131 VGTKLDLRDD 141 KDTIEKLKEK151 KLTPITYPQG161 LAMAKEIGAV171 KYLECSALTQ181 RGLKTVFDEA 191 IRAVLCPPPV201
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:135 or .A:137 or .A:138 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
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| PDB ID: 5O33 A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1 | ||||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [8] |
| PDB Sequence |
MQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 EYIPTVFDNY40 SANVMVDGKP50 VNLGLWDTAG 60 QEDYDRLRPL70 SYPQTDVFLI80 CFSLVSPASF90 ENVRAKWYPE100 VRHHCPNTPI 110 ILVGTKLDLR120 DDKDTIEKLK130 EKKLTPITYP140 QGLAMAKEIG150 AVKYLECSAL 160 TQRGLKTVFD170 EAIRAVL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:33 or .A:57 or .A:59 or .A:62 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
|
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| PDB ID: 1HE1 Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [9] |
| PDB Sequence |
PQAIKCVVVG
10 DGAVGKTCLL20 ISYTTNAFPG30 EYIPTVFDNY40 SANVMVDGKP50 VNLGLWDTAG 60 QEDYDRLRPL70 SYPQTDVFLI80 CFSLVSPASF90 ENVRAKWYPE100 VRHHCPNTPI 110 ILVGTKLDLR120 DDKDTIEKLK130 EKKLTPITYP140 QGLAMAKEIG150 AVKYLECSAL 160 TQRGLKTVFD170 EAIRAV
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:28 or .C:32 or .C:35 or .C:57 or .C:116 or .C:117 or .C:118 or .C:119 or .C:157 or .C:158 or .C:159 or .C:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5N6O Wild type human Rac1-GDP | ||||||
| Method | X-ray diffraction | Resolution | 2.59 Å | Mutation | No | [10] |
| PDB Sequence |
QAIKCVVVGD
11 GAVGKTCLLI21 SYTTNAFPGE31 YIPTVFDNYS41 ANVMVDGKPV51 NLGLWDTAGQ 61 EDYDRLRPLS71 YPQTDVFLIC81 FSLVSPASFE91 NVRAKWYPEV101 RHHCPNTPII 111 LVGTKLDLRD121 DKDTIEKLKE131 KKLTPITYPQ141 GLAMAKEIGA151 VKYLECSALT 161 QRGLKTVFDE171 AIRAVL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .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:33 or .A:57 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:157 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
|
ASP11
3.669
GLY12
3.731
ALA13
2.498
VAL14
3.121
GLY15
2.954
LYS16
2.953
THR17
2.774
CYS18
2.867
PHE28
3.656
GLY30
3.524
ILE33
3.069
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| 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 | Crystal structure of the Rac1-RhoGDI complex involved in nadph oxidase activation. Biochemistry. 2001 Aug 28;40(34):10007-13. | ||||
| REF 3 | A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium. Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):628-35. | ||||
| REF 4 | Yersinia virulence depends on mimicry of host Rho-family nucleotide dissociation inhibitors. Cell. 2006 Sep 8;126(5):869-80. | ||||
| REF 5 | Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1. Mol Cell. 2000 Dec;6(6):1449-60. | ||||
| REF 6 | Conformational landscape alternations promote oncogenic activities of Ras-related C3 botulinum toxin substrate 1 as revealed by NMR. Sci Adv. 2019 Mar 13;5(3):eaav8945. | ||||
| REF 7 | Alternative splicing of Rac1 generates Rac1b, a self-activating GTPase. J Biol Chem. 2004 Feb 6;279(6):4743-9. | ||||
| REF 8 | A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1 | ||||
| REF 9 | How the Pseudomonas aeruginosa ExoS toxin downregulates Rac. Nat Struct Biol. 2001 Jan;8(1):23-6. | ||||
| REF 10 | Allosteric inhibition of the guanine nucleotide exchange factor DOCK5 by a small molecule. Sci Rep. 2017 Oct 31;7(1):14409. | ||||
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