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

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file
Download list in excel
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 H113 3.29x29 TM3 Van der Waals
plerixafor Y116 3.32x32 TM3 hydrophobic
plerixafor D187 45.51x51 ECL2 polar (charge-charge)
plerixafor Q200 5.39x40 TM5 Van der Waals
plerixafor Y263 6.51x51 TM6 Van der Waals
plerixafor D270 6.58x58 TM6 polar (hydrogen bond)
plerixafor D270 6.58x58 TM6 polar (charge-charge)
plerixafor I273 6.61x61 TM6 Van der Waals
plerixafor L274 6.62x62 TM6 Van der Waals
plerixafor E285 7.28x27 TM7 Van der Waals
plerixafor H289 7.32x31 TM7 Van der Waals
plerixafor I292 7.35x34 TM7 hydrophobic
plerixafor E296 7.39x38 TM7 polar (hydrogen bond)
plerixafor E296 7.39x38 TM7 polar (charge-charge)
plerixafor F300 7.43x42 TM7 Van der Waals

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file

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
3x29 3.29x29 H113
3x32 3.32x32 Y116
ECL2
45x51 45.51x51 D187
TM5
5x40 5.39x40 Q200
TM6
6x51 6.51x51 Y255
6x58 6.58x58 D262
6x61 6.61x61 I265
6x62 6.62x62 L266
TM7
7x27 7.28x27 E277
7x31 7.32x31 H281
7x34 7.35x34 I284
7x38 7.39x38 E288
7x42 7.43x42 F292