Structure information

ACKR3

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

7SK9

SPECIES

Homo sapiens

RESOLUTION

3.700

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
(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 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 L104 2.64x64 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 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 N108 ECL1 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 H121 3.29x29 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 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 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 (charge-assisted 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 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 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 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 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 G220 5.46x461 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 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 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)
(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)
(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 H298 7.36x35 TM7 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 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 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 L305 7.43x42 TM7 hydrophobic

Ligands

(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
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
TM5
5x43 5.42x43 S216
5x461 5.46x461 G220
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 H269
TM7
7x35 7.36x35 H298
7x38 7.39x38 Q301
7x41 7.42x41 S304
7x42 7.43x42 L305