Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T13852 Target Info
Target Name Sphingosine-1-phosphate receptor 1 (S1PR1)
Synonyms Sphingosine 1-phosphate receptor Edg-1; S1P1; S1P receptor Edg-1; S1P receptor 1; Endothelial differentiation G-protein coupled receptor 1; CHEDG1; CD363
Target Type Successful Target
Gene Name S1PR1
Biochemical Class GPCR rhodopsin
UniProt ID
S1PR1_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Ozanimod Ligand Info
Structure Description Cryo-EM structure of ozanimod -bound Sphingosine-1-phosphate receptor 1 in complex with Gi protein PDB:7EW0
Method Electron microscopy Resolution 3.42 Å Mutation No [1]
PDB Sequence
YDIIVRHYNY
31
TGKLTSVVFI
53
LICCFIILEN
63
IFVLLTIWKT
73
KKFHRPMYYF
83

IGNLALSDLL
93
AGVAYTANLL
103
LSGATTYKLT
113
PAQWFLREGS
123
MFVALSASVF
133

SLLAIAIERY
143
ITMLKMKLHN
153
GSNNFRLFLL
163
ISACWVISLI
173
LGGLPIMGWN
183

CISALSSCST
193
VLPLYHKHYI
203
LFCTTVFTLL
213
LLSIVILYCR
223
IYSLVRTRSR
233

RLTFRKSEKS
251
LALLKTVIIV
261
LSVFIACWAP
271
LFILLLLDVG
281
CKVKTCDILF
291

RAEYFLVLAV
301
LNSGTNPIIY
311
TLTNKEMRRA
321
FIRI
Residue
Distance (Å)
LYS34
2.543
ASN101
4.479
GLU121
3.453
MET124
3.486
PHE125
3.134
LEU128
3.660
SER129
3.065
VAL132
4.559
VAL194
3.323
LEU195
3.332
ILE203
4.435
Residue
Distance (Å)
CYS206
3.002
THR207
3.096
VAL209
4.284
PHE210
3.611
LEU213
4.014
TRP269
4.136
LEU272
4.226
LEU276
3.531
ALA293
4.966
GLU294
4.149
LEU297
3.824
Ligand Name: Cenerimod Ligand Info
Structure Description Cryo-EM structure of cenerimod -bound Sphingosine-1-phosphate receptor 1 in complex with Gi protein PDB:7EVZ
Method Electron microscopy Resolution 3.07 Å Mutation No [1]
PDB Sequence
YDIIVRHYNY
31
TGKLTSVVFI
53
LICCFIILEN
63
IFVLLTIWKT
73
KKFHRPMYYF
83

IGNLALSDLL
93
AGVAYTANLL
103
LSGATTYKLT
113
PAQWFLREGS
123
MFVALSASVF
133

SLLAIAIERY
143
ITMLKMKLHN
153
GSNNFRLFLL
163
ISACWVISLI
173
LGGLPIMGWN
183

CISALSSCST
193
VLPLYHKHYI
203
LFCTTVFTLL
213
LLSIVILYCR
223
IYSLVRTRSR
233

RLTFRKNISE
249
KSLALLKTVI
259
IVLSVFIACW
269
APLFILLLLD
279
VGCKVKTCDI
289

LFRAEYFLVL
299
AVLNSGTNPI
309
IYTLTNKEMR
319
RAFIRI
Residue
Distance (Å)
LYS34
2.280
ASN101
4.030
SER105
4.754
GLU121
2.688
MET124
3.608
PHE125
2.769
LEU128
3.659
SER129
3.218
VAL132
3.992
PHE133
4.796
LEU174
4.122
VAL194
3.007
LEU195
4.135
Residue
Distance (Å)
CYS206
3.820
VAL209
3.830
PHE210
4.281
LEU213
4.638
TRP269
3.035
LEU272
3.620
PHE273
4.244
LEU275
4.319
LEU276
3.677
ALA293
4.262
GLU294
4.566
LEU297
4.179
Ligand Name: Sphingosine-1-phosphate Ligand Info
Structure Description Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with S1P PDB:7VIE
Method Electron microscopy Resolution 2.86 Å Mutation No [2]
PDB Sequence
DIIVRHYNYT
32
GKTSVVFILI
55
CCFIILENIF
65
VLLTIWKTKK
75
FHRPMYYFIG
85

NLALSDLLAG
95
VAYTANLLLS
105
GATTYKLTPA
115
QWFLREGSMF
125
VALSASVFSL
135

LAIAIERYIT
145
MLKMKLHNGS
155
NNFRLFLLIS
165
ACWVISLILG
175
GLPIMGWNCI
185

SALSSCSTVL
195
PLYHKHYILF
205
CTTVFTLLLL
215
SIVILYCRIY
225
SLVRTRSRRL
235

TFEKSLALLK
256
TVIIVLSVFI
266
ACWAPLFILL
276
LLDVGCKVKT
286
CDILFRAEYF
296

LVLAVLNSGT
306
NPIIYTLTNK
316
EMRRAFIR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S1P or .S1P2 or .S1P3 or :3S1P;style chemicals stick;color identity;select .F:29 or .F:34 or .F:101 or .F:105 or .F:106 or .F:120 or .F:121 or .F:124 or .F:125 or .F:128 or .F:129 or .F:132 or .F:174 or .F:194 or .F:195 or .F:206 or .F:209 or .F:210 or .F:269 or .F:272 or .F:276 or .F:293 or .F:297; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR29
3.658
LYS34
3.528
ASN101
2.959
SER105
3.083
GLY106
3.445
ARG120
4.152
GLU121
3.726
MET124
3.261
PHE125
3.420
LEU128
3.733
SER129
4.010
VAL132
4.812
Residue
Distance (Å)
LEU174
4.415
VAL194
4.127
LEU195
4.576
CYS206
3.729
VAL209
4.203
PHE210
4.123
TRP269
3.919
LEU272
3.534
LEU276
4.018
ALA293
4.349
LEU297
3.494
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (S)-FTY720P Ligand Info
Structure Description Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with (S)-FTY720-P PDB:7VIF
Method Electron microscopy Resolution 2.83 Å Mutation No [2]
PDB Sequence
DIIVRHYNYT
32
GKLNTSVVFI
53
LICCFIILEN
63
IFVLLTIWKT
73
KKFHRPMYYF
83

IGNLALSDLL
93
AGVAYTANLL
103
LSGATTYKLT
113
PAQWFLREGS
123
MFVALSASVF
133

SLLAIAIERY
143
ITMLKMKLHN
153
GSNNFRLFLL
163
ISACWVISLI
173
LGGLPIMGWN
183

CISALSSCST
193
VLPLYHKHYI
203
LFCTTVFTLL
213
LLSIVILYCR
223
IYSLVRTRSR
233

RLTFEKSLAL
254
LKTVIIVLSV
264
FIACWAPLFI
274
LLLLDVGCKV
284
KTCDILFRAE
294

YFLVLAVLNS
304
GTNPIIYTLT
314
NKEMRRAFIR
324
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .J89 or .J892 or .J893 or :3J89;style chemicals stick;color identity;select .F:29 or .F:34 or .F:101 or .F:105 or .F:106 or .F:109 or .F:120 or .F:121 or .F:124 or .F:125 or .F:128 or .F:129 or .F:132 or .F:194 or .F:195 or .F:210 or .F:269 or .F:272 or .F:276 or .F:293 or .F:297; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR29
3.398
LYS34
4.549
ASN101
2.412
SER105
3.389
GLY106
3.184
THR109
3.182
ARG120
3.655
GLU121
3.410
MET124
4.563
PHE125
3.643
LEU128
3.934
Residue
Distance (Å)
SER129
3.637
VAL132
4.502
VAL194
4.453
LEU195
4.485
PHE210
4.186
TRP269
3.468
LEU272
3.635
LEU276
3.981
ALA293
4.888
LEU297
3.368
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: W146 Ligand Info
Structure Description Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A PDB:3V2Y
Method X-ray diffraction Resolution 2.80 Å Mutation Yes [3]
PDB Sequence
VSDYVNYDII
25
VRHYNYTGKL
35
NISADKENSI
45
KLTSVVFILI
55
CCFIILENIF
65

VLLTIWKTKK
75
FHRPMYYFIG
85
NLALSDLLAG
95
VAYTANLLLS
105
GATTYKLTPA
115

QWFLREGSMF
125
VALSASVFSL
135
LAIAIERYIT
145
MLKNNFRLFL
162
LISACWVISL
172

ILGGLPIMGW
182
NCISALSSCS
192
TVLPLYHKHY
202
ILFCTTVFTL
212
LLLSIVILYC
222

RIYSLVRTRN
1002
IFEMLRIDEG
1012
LRLKIYKDTE
1022
GYYTIGIGHL
1032
LTKSPSLNAA
1042

KSELDKAIGR
1052
NTNGVITKDE
1062
AEKLFNQDVD
1072
AAVRGILRNA
1082
KLKPVYDSLD
1092

AVRRAALINM
1102
VFQMGETGVA
1112
GFTNSLRMLQ
1122
QKRWDEAAVN
1132
LAKSRWYNQT
1142

PNRAKRVITT
1152
FRTGTWDAYA
245
SRSSENVALL
255
KTVIIVLSVF
265
IACWAPLFIL
275

LLLDVGCKVK
285
TCDILFRAEY
295
FLVLAVLNSG
305
TNPIIYTLTN
315
KEMRRAFIRI
325

MGRPL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ML5 or .ML52 or .ML53 or :3ML5;style chemicals stick;color identity;select .A:29 or .A:34 or .A:98 or .A:101 or .A:105 or .A:109 or .A:117 or .A:120 or .A:121 or .A:124 or .A:125 or .A:128 or .A:194 or .A:195 or .A:196 or .A:203 or .A:206 or .A:207 or .A:210 or .A:269 or .A:272 or .A:273 or .A:276 or .A:294 or .A:297 or .A:301; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR29
3.403
LYS34
3.441
TYR98
4.123
ASN101
3.299
SER105
3.685
THR109
4.268
TRP117
4.424
ARG120
2.559
GLU121
2.698
MET124
3.361
PHE125
3.431
LEU128
3.438
VAL194
3.278
Residue
Distance (Å)
LEU195
4.865
PRO196
4.092
ILE203
4.605
CYS206
3.604
THR207
4.155
PHE210
4.304
TRP269
3.724
LEU272
4.008
PHE273
4.351
LEU276
3.477
GLU294
3.570
LEU297
3.430
VAL301
4.024
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: SEW2871 Ligand Info
Structure Description Cryo-EM structure of SEW2871-bound Sphingosine-1-phosphate receptor 1 in complex with Gi protein PDB:7EW7
Method Electron microscopy Resolution 3.27 Å Mutation No [1]
PDB Sequence
YDIIVRHYNY
31
TGKLKLTSVV
51
FILICCFIIL
61
ENIFVLLTIW
71
KTKKFHRPMY
81

YFIGNLALSD
91
LLAGVAYTAN
101
LLLSGATTYK
111
LTPAQWFLRE
121
GSMFVALSAS
131

VFSLLAIAIE
141
RYITMLKMKL
151
HNGSNNFRLF
161
LLISACWVIS
171
LILGGLPIMG
181

WNCISALSSC
191
STVLPLYHKH
201
YILFCTTVFT
211
LLLLSIVILY
221
CRIYSLVRTR
231

SRRLTFRKSE
249
KSLALLKTVI
259
IVLSVFIACW
269
APLFILLLLD
279
VGCKVKTCDI
289

LFRAEYFLVL
299
AVLNSGTNPI
309
IYTLTNKEMR
319
RAFIRI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JEX or .JEX2 or .JEX3 or :3JEX;style chemicals stick;color identity;select .D:101 or .D:121 or .D:124 or .D:125 or .D:128 or .D:129 or .D:132 or .D:194 or .D:195 or .D:206 or .D:207 or .D:209 or .D:210 or .D:269 or .D:272 or .D:273 or .D:276 or .D:297; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN101
2.707
GLU121
2.686
MET124
3.458
PHE125
3.176
LEU128
3.200
SER129
3.347
VAL132
3.705
VAL194
4.600
LEU195
3.096
Residue
Distance (Å)
CYS206
4.329
THR207
4.526
VAL209
4.866
PHE210
3.528
TRP269
3.627
LEU272
3.892
PHE273
4.634
LEU276
2.815
LEU297
3.998
Ligand Name: 1-[[4-[(E)-N-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-C-methylcarbonimidoyl]-2-ethylphenyl]methyl]azetidine-3-carboxylic acid Ligand Info
Structure Description Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod PDB:7TD4
Method Electron microscopy Resolution 2.60 Å Mutation Yes [4]
PDB Sequence
DYVNYDIIVR
27
HYNYTGKLNI
45
KLTSVVFILI
55
CCFIILENIF
65
VLLTIWKTKK
75

FHRPMYYFIG
85
NLALSDLLAG
95
VAYTANLLLS
105
GATTYKLTPA
115
QWFLREGSMF
125

VALSASVFSL
135
LAIAIERYIT
145
MLKMKLHNGS
155
NNFRLFLLIS
165
ACWVISLILG
175

GLPIMGWNCI
185
SALSSCSTVL
195
PLYHKHYILF
205
CTTVFTLLLL
215
SIVILYCRIY
225

SLVRTRSRRL
235
TFRKSEKSLA
253
LLKTVIIVLS
263
VFIACWAPLF
273
ILLLLDVGCK
283

VKTCDILFRA
293
EYFLVLAVLN
303
SGTNPIIYTL
313
TNKEMRRAFI
323
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .J8C or .J8C2 or .J8C3 or :3J8C;style chemicals stick;color identity;select .R:29 or .R:34 or .R:101 or .R:105 or .R:106 or .R:109 or .R:120 or .R:121 or .R:124 or .R:125 or .R:128 or .R:129 or .R:132 or .R:133 or .R:174 or .R:194 or .R:195 or .R:206 or .R:207 or .R:209 or .R:210 or .R:213 or .R:269 or .R:272 or .R:276 or .R:293 or .R:294 or .R:297; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR29
3.622
LYS34
3.508
ASN101
3.273
SER105
3.348
GLY106
4.038
THR109
2.935
ARG120
3.227
GLU121
3.446
MET124
4.089
PHE125
3.568
LEU128
3.540
SER129
3.483
VAL132
3.906
PHE133
4.222
Residue
Distance (Å)
LEU174
3.817
VAL194
3.780
LEU195
3.486
CYS206
2.993
THR207
3.591
VAL209
3.610
PHE210
3.597
LEU213
3.681
TRP269
3.834
LEU272
4.325
LEU276
2.838
ALA293
4.225
GLU294
3.965
LEU297
3.628
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: S1p receptor agonist 1 Ligand Info
Structure Description Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307 PDB:7VIG
Method Electron microscopy Resolution 2.89 Å Mutation No [2]
PDB Sequence
DIIVRHYNYT
32
GKLNTSVVFI
53
LICCFIILEN
63
IFVLLTIWKT
73
KKFHRPMYYF
83

IGNLALSDLL
93
AGVAYTANLL
103
LSGATTYKLT
113
PAQWFLREGS
123
MFVALSASVF
133

SLLAIAIERY
143
ITMLKMKLHN
153
GSNNFRLFLL
163
ISACWVISLI
173
LGGLPIMGWN
183

CISALSSCST
193
VLPLYHKHYI
203
LFCTTVFTLL
213
LLSIVILYCR
223
IYSLVRTRSR
233

RLTFEKSLAL
254
LKTVIIVLSV
264
FIACWAPLFI
274
LLLLDVGCKV
284
KTCDILFRAE
294

YFLVLAVLNS
304
GTNPIIYTLT
314
NKEMRRAFIR
324
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7I4 or .7I42 or .7I43 or :37I4;style chemicals stick;color identity;select .F:29 or .F:34 or .F:101 or .F:105 or .F:106 or .F:109 or .F:117 or .F:120 or .F:121 or .F:124 or .F:125 or .F:128 or .F:129 or .F:132 or .F:174 or .F:194 or .F:195 or .F:206 or .F:209 or .F:210 or .F:213 or .F:269 or .F:272 or .F:276 or .F:293 or .F:297; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR29
2.930
LYS34
4.504
ASN101
2.349
SER105
3.828
GLY106
3.173
THR109
3.423
TRP117
4.977
ARG120
3.673
GLU121
3.889
MET124
3.908
PHE125
3.607
LEU128
3.135
SER129
2.794
Residue
Distance (Å)
VAL132
4.943
LEU174
4.763
VAL194
3.716
LEU195
3.964
CYS206
4.424
VAL209
4.748
PHE210
4.218
LEU213
4.577
TRP269
3.906
LEU272
4.020
LEU276
3.751
ALA293
4.799
LEU297
3.359
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Structures of signaling complexes of lipid receptors S1PR1 and S1PR5 reveal mechanisms of activation and drug recognition. Cell Res. 2021 Dec;31(12):1263-1274.
REF 2 Structural insights into sphingosine-1-phosphate receptor activation. Proc Natl Acad Sci U S A. 2022 Apr 19;119(16):e2117716119.
REF 3 Crystal structure of a lipid G protein-coupled receptor. Science. 2012 Feb 17;335(6070):851-5.
REF 4 Differential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate. Nat Commun. 2022 Feb 8;13(1):731.

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