PDB
8U4O
Resolution
3.3 Å
Released
March 13, 2024
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Function
Stromal cell-derived factor 1
Agonist
Reference
10.1038/S41594-024-01397-1

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Ligand Amino Acid Generic Number Segment Interaction Type
Stromal cell-derived factor 1 K25 N-term Van der Waals
Stromal cell-derived factor 1 E26 N-term Van der Waals
Stromal cell-derived factor 1 P27 N-term hydrophobic
Stromal cell-derived factor 1 C28 N-term Van der Waals
Stromal cell-derived factor 1 F29 N-term Van der Waals
Stromal cell-derived factor 1 R30 1.24x24 TM1 Van der Waals
Stromal cell-derived factor 1 N37 1.31x31 TM1 Van der Waals
Stromal cell-derived factor 1 L41 1.35x35 TM1 hydrophobic
Stromal cell-derived factor 1 W94 2.60x60 TM2 Van der Waals
Stromal cell-derived factor 1 D97 2.63x63 TM2 polar (charge-charge)
Stromal cell-derived factor 1 A98 2.64x64 TM2 Van der Waals
Stromal cell-derived factor 1 H113 3.29x29 TM3 Van der Waals
Stromal cell-derived factor 1 Y116 3.32x32 TM3 Van der Waals
Stromal cell-derived factor 1 I185 ECL2 Van der Waals
Stromal cell-derived factor 1 C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 D187 45.51x51 ECL2 polar (charge-charge)
Stromal cell-derived factor 1 D187 45.51x51 ECL2 hydrophobic
Stromal cell-derived factor 1 D187 45.51x51 ECL2 polar (hydrogen bond)
Stromal cell-derived factor 1 F189 ECL2 Van der Waals
Stromal cell-derived factor 1 D193 ECL2 polar (charge-charge)
Stromal cell-derived factor 1 Y255 6.51x51 TM6 Van der Waals
Stromal cell-derived factor 1 D262 6.58x58 TM6 polar (charge-charge)
Stromal cell-derived factor 1 L266 6.62x62 TM6 Van der Waals
Stromal cell-derived factor 1 H281 7.32x31 TM7 Van der Waals
Stromal cell-derived factor 1 I284 7.35x34 TM7 Van der Waals
Stromal cell-derived factor 1 S285 7.36x35 TM7 Van der Waals
Stromal cell-derived factor 1 E288 7.39x38 TM7 polar (hydrogen bond)
Stromal cell-derived factor 1 F292 7.43x42 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
TM1
1x24 1.24x24 R30
1x31 1.31x31 N37
1x35 1.35x35 L41
TM2
2x60 2.60x60 W94
2x63 2.63x63 D97
2x64 2.64x64 A98
TM3
3x29 3.29x29 H113
3x32 3.32x32 Y116
ECL2
45x50 45.50x50 C186
45x51 45.51x51 D187
TM6
6x51 6.51x51 Y255
6x58 6.58x58 D262
6x62 6.62x62 L266
TM7
7x31 7.32x31 H281
7x34 7.35x34 I284
7x35 7.36x35 S285
7x38 7.39x38 E288
7x42 7.43x42 F292