PDB
8ZPN
Resolution
3.3 Å
Released
Feb. 26, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
plerixafor
Function
Antagonist
Reference
10.1073/PNAS.2425795122

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Ligand Amino Acid Generic Number Segment Interaction Type
plerixafor W94 2.60x60 TM2 hydrophobic
plerixafor Y116 3.32x32 TM3 hydrophobic
plerixafor D270 6.58x58 TM6 polar (charge-assisted hydrogen bond)
plerixafor L274 6.62x62 TM6 Van der Waals
plerixafor L274 6.62x62 TM6 hydrophobic
plerixafor H289 7.32x31 TM7 Van der Waals
plerixafor I292 7.35x34 TM7 hydrophobic
plerixafor I292 7.35x34 TM7 Van der Waals
plerixafor E296 7.39x38 TM7 polar (charge-assisted hydrogen bond)
plerixafor F300 7.43x42 TM7 Van der Waals
plerixafor F300 7.43x42 TM7 hydrophobic

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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
TM2
2x60 2.60x60 W94
TM3
3x32 3.32x32 Y116
TM6
6x58 6.58x58 D262
6x62 6.62x62 L266
TM7
7x31 7.32x31 H281
7x34 7.35x34 I284
7x38 7.39x38 E288
7x42 7.43x42 F292