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

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file
Download list in excel
Ligand Amino Acid Generic Number Segment Interaction Type
SDV1a W94 2.60x60 TM2 hydrophobic
SDV1a H113 3.29x29 TM3 polar (hydrogen bond)
SDV1a Y116 3.32x32 TM3 Van der Waals
SDV1a C186 45.50x50 ECL2 Van der Waals
SDV1a C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
SDV1a D187 45.51x51 ECL2 Van der Waals
SDV1a S285 7.36x35 TM7 Van der Waals
SDV1a E288 7.39x38 TM7 polar (charge-assisted hydrogen bond)
SDV1a F292 7.43x42 TM7 hydrophobic
SDV1a F292 7.43x42 TM7 Van der Waals

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file

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
TM3
3x29 3.29x29 H113
3x32 3.32x32 Y116
ECL2
45x50 45.50x50 C186
45x51 45.51x51 D187
TM7
7x35 7.36x35 S285
7x38 7.39x38 E288
7x42 7.43x42 F292