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

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Ligand Amino Acid Generic Number Segment Interaction Type
JDTic W124 23.50x50 ECL1 aromatic (face-to-face)
JDTic D138 3.32x32 TM3 polar (charge-assisted hydrogen bond)
JDTic Y139 3.33x33 TM3 hydrophobic
JDTic Y139 3.33x33 TM3 Van der Waals
JDTic M142 3.36x36 TM3 hydrophobic
JDTic M142 3.36x36 TM3 Van der Waals
JDTic C210 45.50x50 ECL2 Van der Waals
JDTic V230 5.42x43 TM5 Van der Waals
Nanobody 6 L253 5.65x65 TM5 hydrophobic
Nanobody 6 K254 5.66x66 TM5 polar (hydrogen bond with backbone)
Nanobody 6 K254 5.66x66 TM5 Van der Waals
Nanobody 6 V256 5.68x68 TM5 Van der Waals
Nanobody 6 R257 ICL3 polar (charge-assisted hydrogen bond)
Nanobody 6 R257 ICL3 polar (hydrogen bond with backbone)
Nanobody 6 L258 ICL3 hydrophobic
Nanobody 6 L258 ICL3 Van der Waals
Nanobody 6 R263 6.24x24 TM6 Van der Waals
Nanobody 6 D266 6.27x27 TM6 polar (charge-assisted hydrogen bond)
Nanobody 6 R267 6.28x28 TM6 Van der Waals
Nanobody 6 R270 6.31x31 TM6 polar (charge-assisted hydrogen bond)
Nanobody 6 T273 6.34x34 TM6 Van der Waals
Nanobody 6 R274 6.35x35 TM6 Van der Waals
Nanobody 6 L277 6.38x38 TM6 Van der Waals
JDTic W287 6.48x48 TM6 hydrophobic
JDTic W287 6.48x48 TM6 Van der Waals
JDTic H291 6.52x52 TM6 Van der Waals
JDTic H291 6.52x52 TM6 aromatic (edge-to-face)
JDTic I294 6.55x55 TM6 hydrophobic
JDTic I294 6.55x55 TM6 Van der Waals
JDTic I316 7.39x38 TM7 hydrophobic
JDTic G319 7.42x41 TM7 Van der Waals
JDTic Y320 7.43x42 TM7 polar (hydrogen bond)

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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
ECL1
23x50 23.50x50 W124
TM3
3x32 3.32x32 D138
3x33 3.33x33 Y139
3x36 3.36x36 M142
ECL2
45x50 45.50x50 C210
TM5
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
6x52 6.52x52 H291
6x55 6.55x55 I294
TM7
7x38 7.39x38 I316
7x41 7.42x41 G319
7x42 7.43x42 Y320