PDB
9UPV
Resolution
2.7 Å
Released
April 29, 2026
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
SDV1a
Function
Agonist
Reference
10.1101/2025.07.08.663251

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Ligand Amino Acid Generic Number Segment Interaction Type
SDV1a W94 2.60x60 TM2 hydrophobic
SDV1a D97 2.63x63 TM2 polar (charge-assisted hydrogen bond)
SDV1a A98 2.64x64 TM2 Van der Waals
SDV1a A98 2.64x64 TM2 hydrophobic
SDV1a H113 3.29x29 TM3 Van der Waals
SDV1a Y116 3.32x32 TM3 Van der Waals
SDV1a Y116 3.32x32 TM3 hydrophobic
SDV1a C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
SDV1a C186 45.50x50 ECL2 Van der Waals
SDV1a D187 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
SDV1a D262 6.58x58 TM6 polar (charge-assisted hydrogen bond)
SDV1a L266 6.62x62 TM6 Van der Waals
SDV1a H281 7.32x31 TM7 polar (hydrogen bond)
SDV1a I284 7.35x34 TM7 hydrophobic
SDV1a S285 7.36x35 TM7 Van der Waals
SDV1a E288 7.39x38 TM7 polar (charge-assisted hydrogen bond)
SDV1a F292 7.43x42 TM7 hydrophobic

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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
2x64 2.64x64 A98
TM3
3x29 3.29x29 H113
3x32 3.32x32 Y116
ECL2
45x50 45.50x50 C186
45x51 45.51x51 D187
TM6
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