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 T10491 Target Info
Target Name C-X-C chemokine receptor type 7 (ACKR3)
Synonyms RDC1; RDC-1; Gprotein coupled receptor RDC1 homolog; Gprotein coupled receptor 159; GPR159; G-protein coupled receptor RDC1 homolog; G-protein coupled receptor 159; Chemokine orphan receptor 1; CXCR7; CXCR-7; CXC-R7; CXC chemokine receptor type 7; CMKOR1; Atypical chemokine receptor 3
Target Type Preclinical Target
Gene Name ACKR3
Biochemical Class GPCR rhodopsin
UniProt ID
ACKR3_HUMAN
Ligand General Information  Top
Ligand Name Cholesterol Ligand Info
Canonical SMILES CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
InChI 1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKey HVYWMOMLDIMFJA-DPAQBDIFSA-N
PubChem Compound ID 5997
Drug Binding Sites of Target  Top
PDB ID: 7SK4      Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab
Method Electron microscopy Resolution 3.30 Å Mutation Yes [1]
PDB Sequence
IVVDTVMCPN
36
MPNKSVLLYT
46
LSFIYIFIFV
56
IGMIANSVVV
66
WVNIQAKTTG
76

YDTHCYILNL
86
AIADLWVVLT
96
IPVWVVSLVQ
106
HNQWPMGELT
116
CKVTHLIFSI
126

NLFGSIFFLT
136
CMSVDRYLSI
146
TYFTNTPSSR
156
KKMVRRVVCI
166
LVWLLAFCVS
176

LPDTYYLKTV
186
TSASNNETYC
196
RSFYPEHSIK
206
EWLIGMELVS
216
VVLGFAVPFS
226

IIAVFYFLLA
236
RAISASSDQE
246
KHSSRKIIFS
256
YVVVFLVCWL
266
PYHVAVLLDI
276

FSILHYIPFT
286
CRLEHALFTA
296
LHVTQCLSLV
306
HCCVNPVLYS
316
FINRNYRYEL
326

MKAFI
Residue
Distance (Å)
CYS81
4.663
TYR82
4.655
LEU84
3.394
ASN85
2.776
ILE88
2.397
TRP92
2.904
LEU122
3.649
ILE123
2.884
ILE126
2.619
ASN127
2.580
ILE132
4.746
PHE133
2.474
THR136
2.618
CYS137
2.530
VAL140
2.844
LEU144
2.554
Residue
Distance (Å)
TYR148
3.050
PHE149
2.270
VAL160
2.528
ARG162
4.674
VAL164
2.433
CYS165
2.998
ILE166
3.858
LEU167
4.273
VAL168
3.608
TRP169
2.740
LEU171
2.993
PHE173
3.893
LEU219
3.466
VAL223
2.300
PRO224
2.840
ILE227
2.987
PDB ID: 7SK7      Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab
Method Electron microscopy Resolution 3.30 Å Mutation No [1]
PDB Sequence
CIVVDTVMCP
35
NMPNKSVLLY
45
TLSFIYIFIF
55
VIGMIANSVV
65
VWVNIQHCYI
83

LNLAIADLWV
93
VLTIPVWVVS
103
LVQHNQWPMG
113
ELTCKVTHLI
123
FSINLFGSIF
133

FLTCMSVDRY
143
LSITYRKKMV
160
RRVVCILVWL
170
LAFCVSLPDT
180
YYLKTVTSAS
190

NNETYCRSFY
200
PEHSIKEWLI
210
GMELVSVVLG
220
FAVPFSIIAV
230
FYFLLARSRK
252

IIFSYVVVFL
262
VCWLPYHVAV
272
LLDIFSILHY
282
IPFTCRLEHA
292
LFTALHVTQC
302

LSLVHCCVNP
312
VLYSFIN
Residue
Distance (Å)
CYS81
4.585
LEU84
3.385
ASN85
2.930
ILE88
2.236
ALA89
4.951
TRP92
3.326
VAL119
3.095
LEU122
2.241
Residue
Distance (Å)
ILE123
2.367
ILE126
2.379
ASN127
2.521
ARG162
2.026
ILE166
4.245
TRP169
2.704
PHE173
3.325
PDB ID: 7SK8      Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab
Method Electron microscopy Resolution 3.30 Å Mutation No [1]
PDB Sequence
CIVVDTVMCP
35
NMPNKSVLLY
45
TLSFIYIFIF
55
VIGMIANSVV
65
VWVNIQAKTT
75

GYDTHCYILN
85
LAIADLWVVL
95
TIPVWVVSLV
105
QHNQWPMGEL
115
TCKVTHLIFS
125

INLFGSIFFL
135
TCMSVDRYLS
145
ITYFTNTPSS
155
RKKMVRRVVC
165
ILVWLLAFCV
175

SLPDTYYLKT
185
VTSASNNETY
195
CRSFYPEHSI
205
KEWLIGMELV
215
SVVLGFAVPF
225

SIIAVFYFLL
235
ARAISASSDQ
245
EKHSSRKIIF
255
SYVVVFLVCW
265
LPYHVAVLLD
275

IFSILHYIPF
285
TCRLEHALFT
295
ALHVTQCLSL
305
VHCCVNPVLY
315
SFINRNYRYE
325

LMKAFI
Residue
Distance (Å)
VAL42
3.793
LEU43
2.428
THR46
2.802
LEU47
3.395
ILE50
2.457
CYS81
3.889
TYR82
4.409
LEU84
2.928
ASN85
2.717
ILE88
2.582
TRP92
2.548
VAL119
4.861
LEU122
2.712
ILE123
2.764
ILE126
2.339
ASN127
2.685
ILE132
4.250
PHE133
2.623
THR136
2.398
CYS137
2.361
VAL140
2.258
LEU144
2.755
TYR148
2.871
PHE149
2.087
VAL160
2.497
ARG162
4.804
VAL164
2.313
CYS165
4.361
ILE166
3.891
LEU167
4.540
VAL168
4.385
TRP169
2.903
LEU171
2.380
PHE173
2.961
CYS174
2.671
VAL175
2.335
Residue
Distance (Å)
PRO178
3.276
SER204
3.222
GLU207
2.286
TRP208
2.568
GLY211
3.052
MET212
2.836
VAL215
2.616
LEU219
2.763
VAL223
2.291
PRO224
2.903
ILE227
2.792
SER250
2.989
LYS252
2.309
ILE253
2.207
SER256
3.325
VAL260
3.510
VAL263
2.839
CYS264
3.763
LEU266
4.517
PRO267
2.275
ALA271
4.901
HIS291
3.372
ALA292
2.377
LEU293
4.735
THR295
2.623
ALA296
2.236
VAL299
2.730
THR300
2.608
CYS302
3.079
LEU303
2.426
VAL306
2.582
CYS309
4.496
VAL310
2.291
VAL313
2.359
LEU314
2.569
ILE318
2.289
PDB ID: 7SK9      Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist CCX662, and an intracellular Fab
Method Electron microscopy Resolution 3.70 Å Mutation No [1]
PDB Sequence
KSVLLYTLSF
49
IYIFIFVIGM
59
IANSVVVWVN
69
IQAKTTGYDT
79
HCYILNLAIA
89

DLWVVLTIPV
99
WVVSLVQHNQ
109
WPMGELTCKV
119
THLIFSINLF
129
GSIFFLTCMS
139

VDRYLSITYF
149
TNTPSSRKKM
159
VRRVVCILVW
169
LLAFCVSLPD
179
TYYLKTVYCR
197

SFYPEHSIKE
207
WLIGMELVSV
217
VLGFAVPFSI
227
IAVFYFLLAR
237
AISASSDQEK
247

HSSRKIIFSY
257
VVVFLVCWLP
267
YHVAVLLDIF
277
SILHYIPFTC
287
RLEHALFTAL
297

HVTQCLSLVH
307
CCVNPVLYSF
317
INRNYRYELM
327
KA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CLR or .CLR2 or .CLR3 or :3CLR;style chemicals stick;color identity;select .A:82 or .A:84 or .A:85 or .A:88 or .A:92 or .A:119 or .A:122 or .A:123 or .A:126 or .A:127 or .A:132 or .A:133 or .A:136 or .A:137 or .A:140 or .A:144 or .A:148 or .A:149 or .A:156 or .A:160 or .A:162 or .A:164 or .A:165 or .A:166 or .A:167 or .A:168 or .A:169 or .A:171 or .A:173 or .A:219 or .A:223 or .A:224 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR82
4.603
LEU84
3.341
ASN85
2.770
ILE88
2.242
TRP92
2.394
VAL119
4.967
LEU122
4.107
ILE123
2.665
ILE126
2.537
ASN127
3.451
ILE132
4.734
PHE133
2.992
THR136
2.818
CYS137
2.750
VAL140
2.194
LEU144
2.665
TYR148
2.617
Residue
Distance (Å)
PHE149
2.702
ARG156
3.574
VAL160
2.250
ARG162
4.731
VAL164
2.467
CYS165
2.992
ILE166
3.031
LEU167
3.054
VAL168
4.572
TRP169
3.132
LEU171
3.609
PHE173
3.916
LEU219
2.519
VAL223
2.631
PRO224
3.499
ILE227
3.101
PDB ID: 7SK3      Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab
Method Electron microscopy Resolution 3.80 Å Mutation No [1]
PDB Sequence
CIVVDTVMCP
35
NMPNKSVLLY
45
TLSFIYIFIF
55
VIGMIANSVV
65
VWVNIQAKTT
75

GYDTHCYILN
85
LAIADLWVVL
95
TIPVWVVSLV
105
QHNQWPMGEL
115
TCKVTHLIFS
125

INLFGSIFFL
135
TCMSVDRYLS
145
ITYFTNTPSS
155
RKKMVRRVVC
165
ILVWLLAFCV
175

SLPDTYYLKT
185
VTSASNNETY
195
CRSFYPEHSI
205
KEWLIGMELV
215
SVVLGFAVPF
225

SIIAVFYFLL
235
ARAISASSDQ
245
EKHSSRKIIF
255
SYVVVFLVCW
265
LPYHVAVLLD
275

IFSILHYIPF
285
TCRLEHALFT
295
ALHVTQCLSL
305
VHCCVNPVLY
315
SFINRNYRYE
325

LMKA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CLR or .CLR2 or .CLR3 or :3CLR;style chemicals stick;color identity;select .A:42 or .A:43 or .A:46 or .A:47 or .A:50 or .A:53 or .A:54 or .A:57 or .A:66 or .A:70 or .A:73 or .A:81 or .A:82 or .A:84 or .A:85 or .A:88 or .A:91 or .A:92 or .A:95 or .A:122 or .A:123 or .A:126 or .A:127 or .A:132 or .A:133 or .A:136 or .A:137 or .A:140 or .A:144 or .A:148 or .A:149 or .A:156 or .A:160 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:167 or .A:168 or .A:169 or .A:171 or .A:173 or .A:174 or .A:175 or .A:178 or .A:203 or .A:204 or .A:207 or .A:208 or .A:211 or .A:212 or .A:215 or .A:219 or .A:223 or .A:224 or .A:227 or .A:250 or .A:252 or .A:253 or .A:256 or .A:260 or .A:262 or .A:263 or .A:264 or .A:266 or .A:267 or .A:270 or .A:271 or .A:274 or .A:288 or .A:289 or .A:291 or .A:292 or .A:293 or .A:295 or .A:296 or .A:299 or .A:300 or .A:302 or .A:303 or .A:306 or .A:307 or .A:309 or .A:310 or .A:313 or .A:314 or .A:318; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
VAL42
3.153
LEU43
3.232
THR46
2.785
LEU47
2.404
ILE50
2.266
PHE53
4.271
ILE54
2.271
ILE57
4.263
VAL66
3.718
ILE70
2.310
LYS73
4.092
CYS81
3.053
TYR82
4.392
LEU84
2.237
ASN85
2.255
ILE88
2.308
LEU91
2.297
TRP92
2.249
LEU95
2.874
LEU122
3.595
ILE123
2.383
ILE126
2.371
ASN127
2.942
ILE132
4.636
PHE133
2.101
THR136
2.346
CYS137
2.783
VAL140
2.336
LEU144
3.100
TYR148
3.167
PHE149
2.620
ARG156
3.953
VAL160
2.278
ARG162
3.442
VAL163
4.631
VAL164
2.495
CYS165
3.055
ILE166
3.661
LEU167
3.311
VAL168
4.407
TRP169
2.589
LEU171
3.185
PHE173
3.712
CYS174
4.357
Residue
Distance (Å)
VAL175
2.870
PRO178
2.304
HIS203
4.965
SER204
2.637
GLU207
2.192
TRP208
2.510
GLY211
2.778
MET212
2.868
VAL215
2.518
LEU219
2.377
VAL223
2.883
PRO224
3.827
ILE227
3.260
SER250
4.760
LYS252
3.476
ILE253
2.411
SER256
2.581
VAL260
2.942
LEU262
4.930
VAL263
2.509
CYS264
3.328
LEU266
2.302
PRO267
2.350
VAL270
2.773
ALA271
3.495
LEU274
3.319
ARG288
3.710
LEU289
3.444
HIS291
4.945
ALA292
2.947
LEU293
2.864
THR295
2.501
ALA296
2.379
VAL299
2.276
THR300
2.945
CYS302
2.249
LEU303
2.267
VAL306
2.342
HIS307
4.664
CYS309
4.288
VAL310
2.306
VAL313
2.300
LEU314
2.281
ILE318
2.673
PDB ID: 7SK5      Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab
Method Electron microscopy Resolution 4.00 Å Mutation No [1]
PDB Sequence
VVDTVMCPNM
37
PNKSVLLYTL
47
SFIYIFIFVI
57
GMIANSVVVW
67
VNIQAKTTGY
77

DTHCYILNLA
87
IADLWVVLTI
97
PVWVVSLVQH
107
NQWPMGELTC
117
KVTHLIFSIN
127

LFGSIFFLTC
137
MSVDRYLSIT
147
YFTNTPSSRK
157
KMVRRVVCIL
167
VWLLAFCVSL
177

PDTYYLKTVT
187
SNNETYCRSF
199
YPEHSIKEWL
209
IGMELVSVVL
219
GFAVPFSIIA
229

VFYFLLARAI
239
SASSDQEKHS
249
SRKIIFSYVV
259
VFLVCWLPYH
269
VAVLLDIFSI
279

LHYIPFTCRL
289
EHALFTALHV
299
TQCLSLVHCC
309
VNPVLYSFIN
319
RNYRYELMKA
329
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CLR or .CLR2 or .CLR3 or :3CLR;style chemicals stick;color identity;select .A:66 or .A:70 or .A:73 or .A:81 or .A:82 or .A:84 or .A:85 or .A:88 or .A:92 or .A:122 or .A:123 or .A:126 or .A:127 or .A:133 or .A:136 or .A:137 or .A:140 or .A:144 or .A:148 or .A:149 or .A:156 or .A:160 or .A:162 or .A:164 or .A:165 or .A:166 or .A:167 or .A:168 or .A:169 or .A:171 or .A:173 or .A:174 or .A:175 or .A:178 or .A:204 or .A:207 or .A:208 or .A:211 or .A:212 or .A:215 or .A:219 or .A:223 or .A:224 or .A:227 or .A:250 or .A:252 or .A:253 or .A:256 or .A:260 or .A:263 or .A:264 or .A:267 or .A:291 or .A:292 or .A:295 or .A:296 or .A:299 or .A:300 or .A:303 or .A:306 or .A:310 or .A:313 or .A:314 or .A:318 or .A:143 or .A:144 or .A:147 or .A:148 or .A:231; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
VAL66
3.717
ILE70
2.553
LYS73
3.610
CYS81
3.163
TYR82
4.221
LEU84
2.275
ASN85
2.049
ILE88
2.302
TRP92
2.274
LEU122
4.567
ILE123
2.416
ILE126
3.568
ASN127
3.035
PHE133
2.146
THR136
2.851
CYS137
3.454
VAL140
2.552
LEU144
2.877
TYR148
3.934
PHE149
2.705
ARG156
4.392
VAL160
2.602
ARG162
2.975
VAL164
2.433
CYS165
2.781
ILE166
2.776
LEU167
3.781
VAL168
4.963
TRP169
2.701
LEU171
3.399
PHE173
4.017
CYS174
3.226
VAL175
2.791
PRO178
2.673
SER204
4.267
Residue
Distance (Å)
GLU207
2.972
TRP208
2.797
GLY211
3.357
MET212
2.310
VAL215
2.619
LEU219
2.265
VAL223
2.461
PRO224
3.386
ILE227
2.655
SER250
3.991
LYS252
2.783
ILE253
2.492
SER256
2.618
VAL260
2.574
VAL263
2.463
CYS264
3.680
PRO267
3.069
HIS291
4.084
ALA292
3.266
THR295
2.825
ALA296
2.368
VAL299
2.816
THR300
2.786
LEU303
2.630
VAL306
3.163
VAL310
2.239
VAL313
3.058
LEU314
2.175
ILE318
3.255
TYR143
3.133
LEU144
2.877
THR147
4.589
TYR148
2.251
PHE231
3.943
References  Top
REF 1 Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Sci Adv. 2022 Jul 15;8(28):eabn8063.

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