PDB
8U4P
Resolution
3.2 Å
Released
March 13, 2024
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Function
plerixafor
Agonist (partial)
Reference
10.1038/S41594-024-01397-1

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Ligand Amino Acid Generic Number Segment Interaction Type
plerixafor Y45 1.39x39 TM1 Van der Waals
plerixafor W94 2.60x60 TM2 aromatic (pi-cation)
plerixafor Y116 3.32x32 TM3 aromatic (pi-cation)
plerixafor V196 5.35x36 TM5 Van der Waals
plerixafor Q200 5.39x40 TM5 Van der Waals
plerixafor D262 6.58x58 TM6 polar (hydrogen bond)
plerixafor D262 6.58x58 TM6 polar (charge-charge)
plerixafor L266 6.62x62 TM6 Van der Waals
plerixafor E277 7.28x27 TM7 Van der Waals
plerixafor V280 7.31x30 TM7 Van der Waals
plerixafor H281 7.32x31 TM7 aromatic (edge-to-face)
plerixafor I284 7.35x34 TM7 hydrophobic
plerixafor E288 7.39x38 TM7 polar (charge-charge)
plerixafor E288 7.39x38 TM7 polar (hydrogen bond)
plerixafor F292 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
CXCR4
TM1
1x39 1.39x39 Y45
TM2
2x60 2.60x60 W94
TM3
3x32 3.32x32 Y116
TM5
5x36 5.35x36 V196
5x40 5.39x40 Q200
TM6
6x58 6.58x58 D262
6x62 6.62x62 L266
TM7
7x27 7.28x27 E277
7x30 7.31x30 V280
7x31 7.32x31 H281
7x34 7.35x34 I284
7x38 7.39x38 E288
7x42 7.43x42 F292