PDB
5LWE
Resolution
2.8 Å
Released
Dec. 7, 2016
Receptor
CCR9
Class
A
Species
Homo sapiens
Ligand
vercirnon
Function
Allosteric antagonist
Reference
10.1038/NATURE20606

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Ligand Amino Acid Generic Number Segment Interaction Type
vercirnon V69 1.53x53 TM1 hydrophobic
vercirnon V72 1.56x56 TM1 hydrophobic
vercirnon Y73 1.57x57 TM1 hydrophobic
vercirnon R78 ICL1 polar (charge-charge)
vercirnon T81 2.37x37 TM2 polar (charge-assisted hydrogen bond)
vercirnon T83 2.39x39 TM2 Van der Waals
vercirnon D84 2.40x40 TM2 polar (charge-charge)
vercirnon L87 2.43x43 TM2 hydrophobic
vercirnon L87 2.43x43 TM2 Van der Waals
vercirnon I140 3.46x46 TM3 Van der Waals
vercirnon I140 3.46x46 TM3 hydrophobic
vercirnon R144 3.50x50 TM3 Van der Waals
vercirnon A255 6.36x36 TM6 hydrophobic
vercirnon A255 6.36x36 TM6 Van der Waals
vercirnon T256 6.37x37 TM6 Van der Waals
vercirnon V259 6.40x40 TM6 Van der Waals
vercirnon V259 6.40x40 TM6 hydrophobic
vercirnon Y317 7.53x53 TM7 Van der Waals
vercirnon Y317 7.53x53 TM7 aromatic (face-to-edge)
vercirnon G321 8.47x47 H8 Van der Waals
vercirnon E322 8.48x48 H8 polar (hydrogen bond with backbone)
vercirnon E322 8.48x48 H8 Van der Waals
vercirnon R323 8.49x49 H8 polar (hydrogen bond with backbone)
vercirnon R323 8.49x49 H8 polar (charge-charge)
vercirnon F324 8.50x50 H8 polar (hydrogen bond with backbone)
vercirnon F324 8.50x50 H8 Van der Waals
vercirnon D327 8.53x53 H8 Van der Waals

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Snake plot — Download: PNG | SVG
ICL1 T R V K ICL1ECL1 Q W K F ECL1ICL2 A M R A H T W ICL2ECL2 Q I K E E S G I A I C T M V Y P S D E S T ECL2ICL3 K K ICL3ECL3 F I S ECL3N-term M T P T D F T S P I P N M A D D Y G S E S T S S M E D Y V N F N F T D F Y C E K N N N-termC-term Q W V S F T R R E G S L K L S S M L L E T T S G A L S L C-term V R Q F A S H F L P P L Y W L V F I V G A L G N S L V I L V Y W Y C T M T D M F L L N L A I A D L L F L V T L P F W A I A A A D Q T F M C K V V N S M Y K M N F Y S C V L L I M C I S V D R Y I A I A Q R E K R L L Y S K M V C F T I W V L A A A L C I P E I L Y S K L K S A V L T L K V I L G F F L P F V V M A C C Y T I I I H T L I Q A S S K H K A L K V T I T V L T V F V L S Q F P Y N C I L L V Q T I D A Y A M N C A V S T N I D I C F Q V T Q T I A F F H S C L N P V L Y V F V G E R L V K L G C F R R D T L K N I S Q A !
Helix box plot — Download: PNG | SVG S N G L A G V I F V L W Y L P P L F H S 1 L N L A I A D L L F L V T L P F W A I A 2 C M I L L V C S Y F N M K Y M S N V V K 3 S K M V C F T I W V L A A A L C I P E 4 Y C C A M V V F P L F F G L I V K L T L V 5 I T V L T V F V L S Q F P Y N C I L L V 6 V P N L C S H F F A I T Q T V Q F C I 7

GPCRdb(A)
GPCRdb(A)
CCR9
TM1
1x53 1.53x53 V69
1x56 1.56x56 V72
1x57 1.57x57 Y73
TM2
2x37 2.37x37 T81
2x39 2.39x39 T83
2x40 2.40x40 D84
2x43 2.43x43 L87
TM3
3x46 3.46x46 I140
3x50 3.50x50 R144
TM6
6x36 6.36x36 V255
6x37 6.37x37 T256
6x40 6.40x40 V259
TM7
7x53 7.53x53 Y317
H8
8x47 8.47x47 G321
8x48 8.48x48 E322
8x49 8.49x49 R323
8x50 8.50x50 F324
8x53 8.53x53 D327