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 T92640 Target Info
Target Name Lysophosphatidic acid receptor 1 (LPAR1)
Synonyms Lysophosphatidic acid receptor Edg-2; LPA1; LPA-1; LPA receptor 1; EDG2; EDG 2 receptor
Target Type Clinical trial Target
Gene Name LPAR1
Biochemical Class GPCR rhodopsin
UniProt ID
LPAR1_HUMAN
Ligand General Information  Top
Ligand Name [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate Ligand Info
Canonical SMILES CCCCCCC1=CC=CC=C1CCCCC(=O)NC(CO)COP(=O)(O)O
InChI 1S/C20H34NO6P/c1-2-3-4-5-10-17-11-6-7-12-18(17)13-8-9-14-20(23)21-19(15-22)16-27-28(24,25)26/h6-7,11-12,19,22H,2-5,8-10,13-16H2,1H3,(H,21,23)(H2,24,25,26)/t19-/m1/s1
InChIKey LYWONSBDWRVEKO-LJQANCHMSA-N
PubChem Compound ID 141702624
Drug Binding Sites of Target  Top
PDB ID: 7YU3      Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556
Method Electron microscopy Resolution 3.50 Å Mutation No [1]
PDB Sequence
QCFYNESIAF
32
FYNRSGKHLA
42
TEWNTVSKLV
52
MGLGITVCIF
62
IMLANLLVMV
72

AIYVNRRFHF
82
PIYYLMANLA
92
AADFFAGLAY
102
FYLMFNTGPN
112
TRRLTVSTWL
122

LRQGLIDTSL
132
TASVANLLAI
142
AIERHITVFR
152
MQLHTRMSNR
162
RVVVVIVVIW
172

TMAIVMGAIP
182
SVGWNCICDI
192
ENCSNMAPLY
202
SDSYLVFWAI
212
FNLVTFVVMV
222

VLYAHIFGYV
232
RQRTMRMDTM
253
MSLLKTVVIV
263
LGAFIICWTP
273
GLVLLLLDVC
283

CPQCDVLAYE
293
KFFLLLAEFN
303
SAMNPIIYSY
313
RDKEMSATFR
323
Residue
Distance (Å)
TYR34
3.171
LYS39
2.642
LEU105
3.617
ASN108
4.207
THR109
3.366
GLY110
4.196
THR113
3.967
ARG124
2.503
GLN125
3.258
ILE128
4.876
ASP129
3.038
LEU132
4.789
MET198
4.696
ALA199
4.033
Residue
Distance (Å)
TYR202
3.245
TYR206
4.651
LEU207
3.566
TRP210
3.290
TRP271
4.919
GLY274
4.117
LEU277
4.722
LEU278
3.256
GLU293
2.930
LYS294
3.188
PHE296
3.942
LEU297
3.445
ALA300
4.600
PDB ID: 7YU4      Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, focused on receptor
Method Electron microscopy Resolution 3.70 Å Mutation No [1]
PDB Sequence
QCFYNESIAF
32
FYNRSGKHLA
42
TEWNTVSKLV
52
MGLGITVCIF
62
IMLANLLVMV
72

AIYVNRRFHP
83
IYYLMANLAA
93
ADFFAGLAYF
103
YLMFNTGPNT
113
RRLTVSTWLL
123

RQGLIDTSLT
133
ASVANLLAIA
143
IERHITVSNR
162
RVVVVIVVIW
172
TMAIVMGAIP
182

SVGWNCICDI
192
ENCSNMAPLY
202
SDSYLVFWAI
212
FNLVTFVVMV
222
VLYAHIFGLL
257

KTVVIVLGAF
267
IICWTPGLVL
277
LLLDVCCPQC
287
DVLAYEKFFL
297
LLAEFNSAMN
307

PIIYSYRDKE
317
MSATFR
Residue
Distance (Å)
TYR34
3.223
LYS39
2.573
LEU105
3.850
ASN108
4.361
THR109
3.307
GLY110
4.379
THR113
3.865
TRP121
4.970
ARG124
2.431
GLN125
3.416
ASP129
2.813
LEU132
4.775
MET198
4.637
ALA199
4.689
Residue
Distance (Å)
TYR202
3.229
TYR206
4.892
LEU207
4.196
TRP210
3.286
TRP271
4.924
GLY274
4.174
LEU277
4.748
LEU278
3.374
GLU293
2.816
LYS294
3.559
PHE296
3.902
LEU297
3.397
ALA300
4.589
PDB ID: 7YU5      Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state1
Method Electron microscopy Resolution 3.70 Å Mutation No [1]
PDB Sequence
QCFYNESIAF
32
FYNRSGKHLA
42
TEWNTVSKLV
52
MGLGITVCIF
62
IMLANLLVMV
72

AIYVNRRFHF
82
PIYYLMANLA
92
AADFFAGLAY
102
FYLMFNTGPN
112
TRRLTVSTWL
122

LRQGLIDTSL
132
TASVANLLAI
142
AIERHITVFR
152
MQLHTRMSNR
162
RVVVVIVVIW
172

TMAIVMGAIP
182
SVGWNCICDI
192
ENCSNMAPLY
202
SDSYLVFWAI
212
FNLVTFVVMV
222

VLYAHIFGYV
232
RQRTMRMDTM
253
MSLLKTVVIV
263
LGAFIICWTP
273
GLVLLLLDVC
283

CPQCDVLAYE
293
KFFLLLAEFN
303
SAMNPIIYSY
313
RDKEMSATFR
323
Residue
Distance (Å)
TYR34
3.275
LYS39
2.718
LEU105
3.575
ASN108
4.196
THR109
3.364
GLY110
4.200
THR113
3.935
ARG124
2.534
GLN125
3.284
ILE128
4.778
ASP129
3.005
LEU132
4.739
MET198
4.625
Residue
Distance (Å)
ALA199
4.040
TYR202
3.873
TYR206
4.711
LEU207
3.568
TRP210
3.308
GLY274
4.116
LEU277
4.526
LEU278
3.273
GLU293
2.910
LYS294
3.179
PHE296
3.944
LEU297
3.439
ALA300
4.652
PDB ID: 7YU6      Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state2
Method Electron microscopy Resolution 3.90 Å Mutation No [1]
PDB Sequence
QCFYNESIAF
32
FYNRSGKHLA
42
TEWNTVSKLV
52
MGLGITVCIF
62
IMLANLLVMV
72

AIYVNRRFHF
82
PIYYLMANLA
92
AADFFAGLAY
102
FYLMFNTGPN
112
TRRLTVSTWL
122

LRQGLIDTSL
132
TASVANLLAI
142
AIERHITVFR
152
MQLHTRMSNR
162
RVVVVIVVIW
172

TMAIVMGAIP
182
SVGWNCICDI
192
ENCSNMAPLY
202
SDSYLVFWAI
212
FNLVTFVVMV
222

VLYAHIFGYV
232
RQRTMRMDTM
253
MSLLKTVVIV
263
LGAFIICWTP
273
GLVLLLLDVC
283

CPQCDVLAYE
293
KFFLLLAEFN
303
SAMNPIIYSY
313
RDKEMSATFR
323
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K6L or .K6L2 or .K6L3 or :3K6L;style chemicals stick;color identity;select .R:34 or .R:39 or .R:105 or .R:108 or .R:109 or .R:110 or .R:113 or .R:124 or .R:125 or .R:128 or .R:129 or .R:132 or .R:198 or .R:199 or .R:202 or .R:206 or .R:207 or .R:210 or .R:271 or .R:274 or .R:277 or .R:278 or .R:293 or .R:294 or .R:296 or .R:297 or .R:300; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR34
3.870
LYS39
2.701
LEU105
3.546
ASN108
4.200
THR109
3.359
GLY110
4.184
THR113
3.964
ARG124
2.547
GLN125
3.244
ILE128
4.768
ASP129
3.034
LEU132
4.610
MET198
4.662
ALA199
4.062
Residue
Distance (Å)
TYR202
3.273
TYR206
4.521
LEU207
3.557
TRP210
3.305
TRP271
4.883
GLY274
4.081
LEU277
4.784
LEU278
3.236
GLU293
2.964
LYS294
3.219
PHE296
3.915
LEU297
3.475
ALA300
4.523
PDB ID: 7YU7      Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state3
Method Electron microscopy Resolution 4.50 Å Mutation No [1]
PDB Sequence
QCFYNESIAF
32
FYNRSGKHLA
42
TEWNTVSKLV
52
MGLGITVCIF
62
IMLANLLVMV
72

AIYVNRRFHF
82
PIYYLMANLA
92
AADFFAGLAY
102
FYLMFNTGPN
112
TRRLTVSTWL
122

LRQGLIDTSL
132
TASVANLLAI
142
AIERHITVFR
152
MQLHTRMSNR
162
RVVVVIVVIW
172

TMAIVMGAIP
182
SVGWNCICDI
192
ENCSNMAPLY
202
SDSYLVFWAI
212
FNLVTFVVMV
222

VLYAHIFGYV
232
RQRTMRMDTM
253
MSLLKTVVIV
263
LGAFIICWTP
273
GLVLLLLDVC
283

CPQCDVLAYE
293
KFFLLLAEFN
303
SAMNPIIYSY
313
RDKEMSATFR
323
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K6L or .K6L2 or .K6L3 or :3K6L;style chemicals stick;color identity;select .R:34 or .R:39 or .R:105 or .R:108 or .R:109 or .R:110 or .R:113 or .R:124 or .R:125 or .R:128 or .R:129 or .R:132 or .R:198 or .R:199 or .R:202 or .R:206 or .R:207 or .R:210 or .R:271 or .R:274 or .R:277 or .R:278 or .R:293 or .R:294 or .R:296 or .R:297 or .R:300; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR34
3.255
LYS39
2.690
LEU105
3.632
ASN108
4.273
THR109
3.377
GLY110
4.210
THR113
4.008
ARG124
2.551
GLN125
3.289
ILE128
4.979
ASP129
3.033
LEU132
4.857
MET198
4.648
ALA199
4.074
Residue
Distance (Å)
TYR202
3.267
TYR206
4.424
LEU207
3.626
TRP210
3.276
TRP271
4.929
GLY274
4.099
LEU277
4.736
LEU278
3.246
GLU293
2.933
LYS294
3.196
PHE296
3.938
LEU297
3.456
ALA300
4.742
References  Top
REF 1 Structure of the active G(i)-coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist. Nat Commun. 2022 Sep 15;13(1):5417.

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