PDB
9MET
Resolution
5.7 Å
Released
Sept. 10, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
HIV-2/gp120
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
HIV-2/gp120 E26 N-term polar (charge-assisted hydrogen bond)
HIV-2/gp120 P27 N-term Van der Waals
HIV-2/gp120 P27 N-term hydrophobic
HIV-2/gp120 F29 N-term hydrophobic
HIV-2/gp120 F29 N-term Van der Waals
HIV-2/gp120 E31 N-term Van der Waals
HIV-2/gp120 S178 ECL2 Van der Waals
HIV-2/gp120 I185 ECL2 Van der Waals
HIV-2/gp120 I185 ECL2 hydrophobic
HIV-2/gp120 D187 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
HIV-2/gp120 R188 45.52x52 ECL2 polar (hydrogen bond with backbone)
HIV-2/gp120 R188 45.52x52 ECL2 Van der Waals
HIV-2/gp120 F189 ECL2 Van der Waals
HIV-2/gp120 F189 ECL2 hydrophobic
HIV-2/gp120 Y190 ECL2 aromatic (face-to-face)
HIV-2/gp120 Y190 ECL2 polar (hydrogen bond with backbone)
HIV-2/gp120 Y190 ECL2 Van der Waals
HIV-2/gp120 P191 ECL2 Van der Waals
HIV-2/gp120 N192 ECL2 polar (hydrogen bond with backbone)
HIV-2/gp120 N192 ECL2 Van der Waals
HIV-2/gp120 D193 5.32x33 TM5 Van der Waals
HIV-2/gp120 V196 5.35x36 TM5 hydrophobic
HIV-2/gp120 V196 5.35x36 TM5 Van der Waals
HIV-2/gp120 F199 5.38x39 TM5 aromatic (face-to-edge)
HIV-2/gp120 F199 5.38x39 TM5 Van der Waals
HIV-2/gp120 Q200 5.39x40 TM5 Van der Waals
HIV-2/gp120 D262 6.58x58 TM6 polar (charge-assisted hydrogen bond)
HIV-2/gp120 E277 7.28x27 TM7 polar (charge-assisted hydrogen bond)
HIV-2/gp120 H281 7.32x31 TM7 polar (hydrogen bond with backbone)
HIV-2/gp120 H281 7.32x31 TM7 polar (hydrogen bond)
HIV-2/gp120 H281 7.32x31 TM7 Van der Waals
HIV-2/gp120 I284 7.35x34 TM7 Van der Waals

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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
TM6
6x58 6.58x58 D262
TM7
7x27 7.28x27 E277
7x31 7.32x31 H281
7x34 7.35x34 I284