PDB
9MEN
Resolution
3.6 Å
Released
Sept. 10, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Surface protein gp120 V3 loop
Function
Agonist
Reference
10.1038/S41467-025-63815-2

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Ligand Amino Acid Generic Number Segment Interaction Type
Surface protein gp120 V3 loop P27 N-term hydrophobic
Surface protein gp120 V3 loop C28 N-term hydrophobic
Surface protein gp120 V3 loop F29 N-term hydrophobic
Surface protein gp120 V3 loop I185 ECL2 hydrophobic
Surface protein gp120 V3 loop D187 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
Surface protein gp120 V3 loop R188 45.52x52 ECL2 Van der Waals
Surface protein gp120 V3 loop R188 45.52x52 ECL2 polar (hydrogen bond with backbone)
Surface protein gp120 V3 loop F189 ECL2 Van der Waals
Surface protein gp120 V3 loop Y190 ECL2 Van der Waals
Surface protein gp120 V3 loop Y190 ECL2 polar (hydrogen bond with backbone)
Surface protein gp120 V3 loop P191 ECL2 Van der Waals
Surface protein gp120 V3 loop N192 ECL2 Van der Waals
Surface protein gp120 V3 loop D193 5.32x33 TM5 Van der Waals
Surface protein gp120 V3 loop V196 5.35x36 TM5 Van der Waals
Surface protein gp120 V3 loop V196 5.35x36 TM5 hydrophobic
Surface protein gp120 V3 loop F199 5.38x39 TM5 hydrophobic
Surface protein gp120 V3 loop F199 5.38x39 TM5 Van der Waals
Surface protein gp120 V3 loop Q200 5.39x40 TM5 Van der Waals
Surface protein gp120 V3 loop H203 5.42x43 TM5 Van der Waals
Surface protein gp120 V3 loop D262 6.58x58 TM6 polar (charge-assisted hydrogen bond)
Surface protein gp120 V3 loop L266 6.62x62 TM6 hydrophobic
Surface protein gp120 V3 loop L266 6.62x62 TM6 Van der Waals
Surface protein gp120 V3 loop E277 7.28x27 TM7 Van der Waals
Surface protein gp120 V3 loop H281 7.32x31 TM7 polar (hydrogen bond)
Surface protein gp120 V3 loop E288 7.39x38 TM7 polar (charge-assisted hydrogen bond)

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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
ECL2
45x51 45.51x51 D187
45x52 45.52x52 R188
TM5
5x33 5.32x33 D193
5x36 5.35x36 V196
5x39 5.38x39 F199
5x40 5.39x40 Q200
5x43 5.42x43 H203
TM6
6x58 6.58x58 D262
6x62 6.62x62 L266
TM7
7x27 7.28x27 E277
7x31 7.32x31 H281
7x38 7.39x38 E288