PDB
6VI4
Resolution
3.3 Å
Released
March 18, 2020
Receptor
κ
Class
A
Species
Homo sapiens
Ligands
Function
JDTic
Inverse agonist
Nanobody 6
NAM
Reference
10.1038/S41467-020-14889-7
JDTic Nanobody 6

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Ligand Amino Acid Generic Number Segment Interaction Type
JDTic V108 2.53x53 TM2 hydrophobic
JDTic T111 2.56x56 TM2 Van der Waals
JDTic Q115 2.60x60 TM2 hydrophobic
JDTic V118 2.63x63 TM2 Van der Waals
JDTic W124 23.50x50 ECL1 hydrophobic
JDTic V134 3.28x28 TM3 hydrophobic
JDTic L135 3.29x29 TM3 Van der Waals
JDTic D138 3.32x32 TM3 polar (charge-charge)
JDTic D138 3.32x32 TM3 hydrophobic
JDTic D138 3.32x32 TM3 polar (hydrogen bond)
JDTic Y139 3.33x33 TM3 hydrophobic
JDTic Y139 3.33x33 TM3 aromatic (pi-cation)
JDTic M142 3.36x36 TM3 hydrophobic
JDTic C210 45.50x50 ECL2 hydrophobic
JDTic K227 5.39x40 TM5 Van der Waals
JDTic V230 5.42x43 TM5 Van der Waals
Nanobody 6 L253 5.65x65 TM5 hydrophobic
Nanobody 6 K254 5.66x66 TM5 Van der Waals
Nanobody 6 V256 5.68x68 TM5 Van der Waals
Nanobody 6 R257 ICL3 polar (charge-charge)
Nanobody 6 R257 ICL3 hydrophobic
Nanobody 6 R257 ICL3 polar (hydrogen bond with backbone)
Nanobody 6 R257 ICL3 polar (hydrogen bond)
Nanobody 6 L258 ICL3 hydrophobic
Nanobody 6 R263 6.24x24 TM6 polar (charge-charge)
Nanobody 6 R263 6.24x24 TM6 hydrophobic
Nanobody 6 D266 6.27x27 TM6 polar (charge-charge)
Nanobody 6 D266 6.27x27 TM6 polar (hydrogen bond)
Nanobody 6 R267 6.28x28 TM6 polar (charge-charge)
Nanobody 6 R267 6.28x28 TM6 hydrophobic
Nanobody 6 R270 6.31x31 TM6 polar (hydrogen bond)
Nanobody 6 T273 6.34x34 TM6 hydrophobic
Nanobody 6 R274 6.35x35 TM6 polar (charge-charge)
Nanobody 6 R274 6.35x35 TM6 hydrophobic
Nanobody 6 L277 6.38x38 TM6 hydrophobic
JDTic W287 6.48x48 TM6 hydrophobic
JDTic I290 6.51x51 TM6 hydrophobic
JDTic H291 6.52x52 TM6 Van der Waals
JDTic I294 6.55x55 TM6 hydrophobic
JDTic I316 7.39x38 TM7 Van der Waals
JDTic G319 7.42x41 TM7 Van der Waals
JDTic Y320 7.43x42 TM7 polar (hydrogen bond)
JDTic Y320 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
κ receptor
TM2
2x53 2.53x53 V108
2x56 2.56x56 T111
2x60 2.60x60 Q115
2x63 2.63x63 V118
ECL1
23x50 23.50x50 W124
TM3
3x28 3.28x28 V134
3x29 3.29x29 I135
3x32 3.32x32 D138
3x33 3.33x33 Y139
3x36 3.36x36 M142
ECL2
45x50 45.50x50 C210
TM5
5x40 5.39x40 K227
5x43 5.42x43 V230
5x65 5.65x65 L253
5x66 5.66x66 K254
5x68 5.68x68 V256
TM6
6x24 6.24x24 R263
6x27 6.27x27 D266
6x28 6.28x28 R267
6x31 6.31x31 R270
6x34 6.34x34 T273
6x35 6.35x35 R274
6x38 6.38x38 L277
6x48 6.48x48 W287
6x51 6.51x51 I290
6x52 6.52x52 H291
6x55 6.55x55 I294
TM7
7x38 7.39x38 I316
7x41 7.42x41 G319
7x42 7.43x42 Y320