PDB
9U4Y
Resolution
2.7 Å
Released
June 11, 2025
Receptor
GnRH1
Class
A
Species
Xenopus laevis
Ligand
CHEMBL266314
Function
Agonist
Reference
10.1073/PNAS.2500112122

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Ligand Amino Acid Generic Number Segment Interaction Type
CHEMBL266314 R56 1.35x35 TM1 polar (charge-assisted hydrogen bond)
CHEMBL266314 L109 2.60x59 TM2 Van der Waals
CHEMBL266314 D110 2.61x60 TM2 polar (charge-assisted hydrogen bond)
CHEMBL266314 W113 2.64x63 TM2 polar (hydrogen bond)
CHEMBL266314 N114 2.65x64 TM2 Van der Waals
CHEMBL266314 L117 ECL1 Van der Waals
CHEMBL266314 L117 ECL1 hydrophobic
CHEMBL266314 M130 3.29x29 TM3 Van der Waals
CHEMBL266314 K133 3.32x32 TM3 polar (charge-assisted hydrogen bond)
CHEMBL266314 L134 3.33x33 TM3 Van der Waals
CHEMBL266314 M137 3.36x36 TM3 polar (hydrogen bond)
CHEMBL266314 Q186 ECL2 Van der Waals
CHEMBL266314 F190 ECL2 polar (hydrogen bond)
CHEMBL266314 V193 ECL2 Van der Waals
CHEMBL266314 Q203 ECL2 Van der Waals
CHEMBL266314 C204 45.50x50 ECL2 Van der Waals
CHEMBL266314 A205 45.51x51 ECL2 polar (hydrogen bond)
CHEMBL266314 T206 45.52x52 ECL2 polar (hydrogen bond with backbone)
CHEMBL266314 T206 45.52x52 ECL2 polar (hydrogen bond)
CHEMBL266314 T206 45.52x52 ECL2 polar (hydrogen bond)
CHEMBL266314 N220 5.39x40 TM5 Van der Waals
CHEMBL266314 T223 5.42x43 TM5 polar (hydrogen bond)
CHEMBL266314 L227 5.46x461 TM5 Van der Waals
CHEMBL266314 Y294 6.51x51 TM6 polar (hydrogen bond)
CHEMBL266314 Y294 6.51x51 TM6 aromatic (edge-to-face)
CHEMBL266314 Y294 6.51x51 TM6 polar (hydrogen bond)
CHEMBL266314 Y295 6.52x52 TM6 polar (hydrogen bond)
CHEMBL266314 G298 6.55x55 TM6 Van der Waals
CHEMBL266314 Y301 6.58x58 TM6 polar (hydrogen bond)
CHEMBL266314 Y301 6.58x58 TM6 aromatic (face-to-edge)
CHEMBL266314 Y301 6.58x58 TM6 polar (hydrogen bond)
CHEMBL266314 W302 6.59x59 TM6 aromatic (edge-to-face)
CHEMBL266314 W302 6.59x59 TM6 polar (hydrogen bond)
CHEMBL266314 M307 ECL3 polar (hydrogen bond)
CHEMBL266314 L308 ECL3 polar (hydrogen bond)
CHEMBL266314 V313 ECL3 polar (hydrogen bond)
CHEMBL266314 P315 7.32x31 TM7 polar (hydrogen bond)
CHEMBL266314 S318 7.35x34 TM7 Van der Waals
CHEMBL266314 F322 7.39x38 TM7 polar (hydrogen bond)

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Snake plot — Download: PNG | SVG
ICL1 K K K ICL1ECL1 Q W Y ECL1ICL2 P L ICL2ECL2 P Q L F V F H T V S R S E P I H F V Q C A T V G S F Q ECL2ICL3 K E I D L R R S S N N I ICL3ECL3 P E M L T E E K V ECL3N-term M L T M S Y Q G I M D S Q D L C A L N R S C F H L K E Q E K T Y G P N I T V L N D K A F I L P T F N-termC-term I H F R R E I R R V C R C A A Q G K D H D T A S V G T G S F R I T T T P A P I K R T V G V L G G S G K F E L E V T G H G L H S G K C D Q C Q G R I V E S F M C-term S T A A K I R V A I T C V L F I F S A C F N I A A L W T I T Y K Y S H I R I L I I N L V A A D L F I T L V V M P L D A V W N V T L A G D L A C R V L M F L K L A A M Y S S A F V T V V I S L D R Q A A I L N G I G D A K K K N K I M L C V A W F L S Y L L A I A H W Q E T I Y N M F T F F C L F L L P L L I M V S C Y T R I L M E I S H K M K A T C V S S P R A R M R T L K M S L V I V L T F I V C W T P Y Y L L G I W Y W F S P P S L S H I L F L F G L L N T C L D P I I Y G L F T
Helix box plot — Download: PNG | SVG I N F C A S F I F L V C T I A V R I K A 1 I N L V A A D L F I T V L V M P L D A V W 2 V V T V F A S S Y M A A L K L F M L V R 3 N K I M L C V A W F L S Y L L A I 4 Y C S V M I L L P L L F L C F F T F M N Y 5 L V I V L T F I V C W T P Y Y L L G I W 6 I P D L C T N L L G F L F L I H S L S 7

GPCRdb(A)
GPCRdb(A)
GnRH1 receptor
TM1
1x35 1.35x35 R56
TM2
2x59 2.60x59 L109
2x60 2.61x60 D110
2x63 2.64x63 W113
2x64 2.65x64 N114
TM3
3x29 3.29x29 M130
3x32 3.32x32 K133
3x33 3.33x33 L134
3x36 3.36x36 M137
ECL2
45x50 45.50x50 C204
45x51 45.51x51 A205
45x52 45.52x52 T206
TM5
5x40 5.39x40 N220
5x43 5.42x43 T223
5x461 5.46x461 L227
TM6
6x51 6.51x51 Y294
6x52 6.52x52 Y295
6x55 6.55x55 G298
6x58 6.58x58 Y301
6x59 6.59x59 W302
TM7
7x31 7.32x31 P315
7x34 7.35x34 S318
7x38 7.39x38 F322