PDB
9MEJ
Resolution
4.0 Å
Released
Sept. 10, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Function
gp120
Agonist
Reference
10.1038/S41467-025-63815-2

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Ligand Amino Acid Generic Number Segment Interaction Type
gp120 E26 N-term Van der Waals
gp120 P27 N-term Van der Waals
gp120 C28 N-term hydrophobic
gp120 F29 N-term Van der Waals
gp120 E31 N-term Van der Waals
gp120 W94 2.60x60 TM2 Van der Waals
gp120 A180 ECL2 Van der Waals
gp120 D181 ECL2 Van der Waals
gp120 I185 ECL2 hydrophobic
gp120 D187 45.51x51 ECL2 polar (hydrogen bond)
gp120 R188 45.52x52 ECL2 aromatic (pi-cation)
gp120 R188 45.52x52 ECL2 hydrophobic
gp120 F189 ECL2 Van der Waals
gp120 Y190 ECL2 polar (hydrogen bond with backbone)
gp120 P191 ECL2 Van der Waals
gp120 N192 5.31x32 TM5 Van der Waals
gp120 D193 5.32x33 TM5 polar (charge-charge)
gp120 V196 5.35x36 TM5 Van der Waals
gp120 Q200 5.39x40 TM5 hydrophobic
gp120 H203 5.42x43 TM5 Van der Waals
gp120 Y255 6.51x51 TM6 Van der Waals
gp120 D262 6.58x58 TM6 polar (charge-charge)
gp120 D262 6.58x58 TM6 polar (hydrogen bond)
gp120 L266 6.62x62 TM6 Van der Waals
gp120 E268 6.64x64 TM6 polar (charge-charge)
gp120 E277 7.28x27 TM7 polar (hydrogen bond)
gp120 E277 7.28x27 TM7 polar (charge-charge)
gp120 H281 7.32x31 TM7 aromatic (edge-to-face)
gp120 E288 7.39x38 TM7 polar (hydrogen bond)
gp120 E288 7.39x38 TM7 polar (charge-charge)

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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
ECL2
45x51 45.51x51 D187
45x52 45.52x52 R188
TM5
5x33 5.32x33 D193
5x36 5.35x36 V196
5x40 5.39x40 Q200
5x43 5.42x43 H203
TM6
6x51 6.51x51 Y255
6x58 6.58x58 D262
6x62 6.62x62 L266
6x64 6.64x64 E268
TM7
7x27 7.28x27 E277
7x31 7.32x31 H281
7x38 7.39x38 E288