Structure information

ACKR3

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

7SK8

SPECIES

Homo sapiens

RESOLUTION

3.300

PREFERRED CHAIN

A

REFERENCE

10.1126/SCIADV.ABN8063

PUBLICATION DATE

July 27, 2022

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
Stromal cell-derived factor 1 I27 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 I27 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 V28 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 V28 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 V29 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 D30 N-term polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 D30 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 T31 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 V32 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 V32 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 M33 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 C34 N-term polar (hydrogen bond)
Stromal cell-derived factor 1 C34 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 P35 N-term Van der Waals
Stromal cell-derived factor 1 N36 N-term polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium Y51 1.39x39 TM1 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium W100 2.60x60 TM2 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S103 2.63x63 TM2 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S103 2.63x63 TM2 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium L104 2.64x64 TM2 Van der Waals
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium N108 ECL1 polar (hydrogen bond)
Stromal cell-derived factor 1 N108 ECL1 Van der Waals
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium W110 23.50x50 ECL1 Van der Waals
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium H121 3.29x29 TM3 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium F124 3.32x32 TM3 aromatic (edge-to-face)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium F124 3.32x32 TM3 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S125 3.33x33 TM3 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium L128 3.36x36 TM3 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium F129 3.37x37 TM3 hydrophobic
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium F129 3.37x37 TM3 Van der Waals
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium I132 3.40x40 TM3 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium D179 4.60x61 TM4 Van der Waals
Stromal cell-derived factor 1 N191 ECL2 Van der Waals
Stromal cell-derived factor 1 Y195 ECL2 polar (hydrogen bond)
Stromal cell-derived factor 1 R197 45.51x51 ECL2 Van der Waals
Stromal cell-derived factor 1 E202 ECL2 Van der Waals
Stromal cell-derived factor 1 I205 5.31x32 TM5 Van der Waals
Stromal cell-derived factor 1 K206 5.32x33 TM5 Van der Waals
Stromal cell-derived factor 1 L209 5.35x36 TM5 Van der Waals
Stromal cell-derived factor 1 L209 5.35x36 TM5 hydrophobic
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S216 5.42x43 TM5 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S216 5.42x43 TM5 polar (hydrogen bond with backbone)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium G220 5.46x461 TM5 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium W265 6.48x48 TM6 hydrophobic
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium W265 6.48x48 TM6 Van der Waals
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium Y268 6.51x51 TM6 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium H269 6.52x52 TM6 polar (hydrogen bond)
Stromal cell-derived factor 1 D275 6.58x58 TM6 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 I279 6.62x62 TM6 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 I279 6.62x62 TM6 polar (hydrogen bond)
Stromal cell-derived factor 1 L280 6.63x63 TM6 polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 L280 6.63x63 TM6 Van der Waals
Stromal cell-derived factor 1 H281 6.64x64 TM6 polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 H281 6.64x64 TM6 polar (hydrogen bond)
Stromal cell-derived factor 1 Y282 ECL3 polar (hydrogen bond)
Stromal cell-derived factor 1 Y282 ECL3 polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 P284 ECL3 Van der Waals
Stromal cell-derived factor 1 F285 ECL3 Van der Waals
Stromal cell-derived factor 1 F285 ECL3 hydrophobic
Stromal cell-derived factor 1 E290 7.28x27 TM7 Van der Waals
Stromal cell-derived factor 1 L293 7.31x30 TM7 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 F294 7.32x31 TM7 Van der Waals
Stromal cell-derived factor 1 L297 7.35x34 TM7 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium Q301 7.39x38 TM7 polar (hydrogen bond with backbone)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium Q301 7.39x38 TM7 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium S304 7.42x41 TM7 polar (hydrogen bond)
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium L305 7.43x42 TM7 hydrophobic
(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium L305 7.43x42 TM7 Van der Waals

Ligands

Stromal cell-derived factor 1

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(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium

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Residue Diagrams

S N A I M G I V F I F I Y I F S L T Y L 1 L N L A I A D L W V V L T I P V W V V S 2 C T L F F I S G F L N I S F I L H T V K 3 R R V V C I L V W L L A F C V S L P D 4 Y F V A I I S F P V A F G L V V S V L E M 5 F S Y V V V F L V C W L P Y H V A V L L 6 V P N V C C H V L S L C Q T V H L A T 7
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ICL1 K T T G ICL1ECL1 H N Q W P M ECL1ICL2 F T N T P S S R K K M ICL2ECL2 K T V T S A S N N E T Y C R S F Y P E H ECL2ICL3 S D ICL3ECL3 Y I P F ECL3N-term M D L H L F D Y S E P G N F S D I S W P C N S S D C I V V D T V M C P N M P N K N-termC-term Y S A K T G L T K L I D A S R V S E T E Y S A L E Q S T K C-term S V L L Y T L S F I Y I F I F V I G M I A N S V V V W V N I Q A Y D T H C Y I L N L A I A D L W V V L T I P V W V V S L V Q G E L T C K V T H L I F S I N L F G S I F F L T C M S V D R Y L S I T Y V R R V V C I L V W L L A F C V S L P D T Y Y L S I K E W L I G M E L V S V V L G F A V P F S I I A V F Y F L L A R A I S A S Q E K H S S R K I I F S Y V V V F L V C W L P Y H V A V L L D I F S I L H T C R L E H A L F T A L H V T Q C L S L V H C C V N P V L Y S F I N R N L M K K Y R Y E A F I F
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Residue Table


GPCRdb(A)
GPCRdb(A)
ACKR3
TM1
1x39 1.39x39 Y51
TM2
2x60 2.60x60 W100
2x63 2.63x63 S103
2x64 2.64x64 L104
ECL1
23x50 23.50x50 W110
TM3
3x29 3.29x29 H121
3x32 3.32x32 F124
3x33 3.33x33 S125
3x36 3.36x36 L128
3x37 3.37x37 F129
3x40 3.40x40 I132
TM4
4x61 4.60x61 D179
ECL2
45x51 45.51x51 R197
TM5
5x32 5.31x32 I205
5x33 5.32x33 K206
5x36 5.35x36 L209
5x43 5.42x43 S216
5x461 5.46x461 G220
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 H269
6x58 6.58x58 D275
6x62 6.62x62 I279
6x63 6.63x63 L280
6x64 6.64x64 H281
TM7
7x27 7.28x27 E290
7x30 7.31x30 L293
7x31 7.32x31 F294
7x34 7.35x34 L297
7x38 7.39x38 Q301
7x41 7.42x41 S304
7x42 7.43x42 L305