PDB
8ZPL
Resolution
3.0 Å
Released
Feb. 26, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Function
CHEMBL5172755
Antagonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
CHEMBL5172755 W94 2.60x60 TM2 aromatic (pi-cation)
CHEMBL5172755 W94 2.60x60 TM2 hydrophobic
CHEMBL5172755 D97 2.63x63 TM2 polar (hydrogen bond)
CHEMBL5172755 D97 2.63x63 TM2 polar (charge-charge)
CHEMBL5172755 W102 23.50x50 ECL1 hydrophobic
CHEMBL5172755 V112 3.28x28 TM3 hydrophobic
CHEMBL5172755 H113 3.29x29 TM3 Van der Waals
CHEMBL5172755 C186 45.50x50 ECL2 hydrophobic
CHEMBL5172755 D187 45.51x51 ECL2 Van der Waals
CHEMBL5172755 R188 45.52x52 ECL2 Van der Waals
CHEMBL5172755 Y190 ECL2 hydrophobic
CHEMBL5172755 V196 5.35x36 TM5 Van der Waals
CHEMBL5172755 Q200 5.39x40 TM5 Van der Waals
CHEMBL5172755 Y263 6.51x51 TM6 Van der Waals
CHEMBL5172755 D270 6.58x58 TM6 polar (charge-charge)
CHEMBL5172755 D270 6.58x58 TM6 polar (hydrogen bond)
CHEMBL5172755 I273 6.61x61 TM6 Van der Waals
CHEMBL5172755 L274 6.62x62 TM6 Van der Waals
CHEMBL5172755 E285 7.28x27 TM7 Van der Waals
CHEMBL5172755 H289 7.32x31 TM7 Van der Waals
CHEMBL5172755 I292 7.35x34 TM7 hydrophobic
CHEMBL5172755 S293 7.36x35 TM7 Van der Waals
CHEMBL5172755 E296 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
2x63 2.63x63 D97
ECL1
23x50 23.50x50 W102
TM3
3x28 3.28x28 V112
3x29 3.29x29 H113
ECL2
45x50 45.50x50 C186
45x51 45.51x51 D187
45x52 45.52x52 R188
TM5
5x36 5.35x36 V196
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
7x35 7.36x35 S285
7x38 7.39x38 E288