Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

Index: hub id, click on each number to highlight the corresponding hub in the 3D visualization.

Hub: the hub being considered.

Avg Int. Strength: the average interaction strength of all the links of the corresponding hub.

Num Of Links: the number of links of the corresponding hub.

Community: the id of the community the link belong to, otherwise 0.

ConSurf: this column reports the ConSurf conservation grades of each hub.

Index Hub Avg Int. Strength Num Of Links Community ConSurf
1L:L:Y1 8.62610
2L:L:?2 10.282510
3L:L:F4 7.41630
4R:R:I52 6.05415
5R:R:Y56 6.45333617
6R:R:Y77 8.67405
7R:R:I86 4.782506
8R:R:Y87 8.962527
9R:R:F89 5.9725406
10R:R:L91 7.05529
11R:R:D95 8.124529
12R:R:Q105 6.9775435
13R:R:W114 8.12738
14R:R:F116 10.384507
15R:R:Y130 6.2565
16R:R:M132 5.6225418
17R:R:F133 5.875407
18R:R:T134 8.6625468
19R:R:M141 6.0225427
20R:R:M142 5.915429
21R:R:Y147 6.562508
22R:R:R160 6.564506
23R:R:W173 10.5825469
24R:R:R190 8.2375473
25R:R:F202 6.32714706
26R:R:K214 6.91405
27R:R:F218 6.5925415
28R:R:F222 6.5475418
29R:R:Y233 6.12571728
30R:R:K252 1.36402
31R:R:F270 7.91419
32R:R:W274 8.98833618
33R:R:I289 3.9425441
34R:R:D293 5.7575403
35R:R:H301 10.665414
36R:R:I304 7.375415
37R:R:Y308 9.595437
38R:R:N310 7.115409
39R:R:N314 8.525429
40R:R:Y318 7.00167629
41R:R:F325 8.864558
   

Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

Index: link id, click on each number to highlight the corresponding link in the 3D visualization.

Node1 Node2: the two nodes of the corresponding link.

Recurrence: the relative Recurrence in the pool of shortest paths.

Int. Strength: the interaction strength between the two nodes.

Hub1?, Hub2?: "Yes" if the corresponding node has more than 3 links, otherwise "No".

Community: the id of the community the link belong to, otherwise 0.

ConSurf1, ConSurf2: these columns report the ConSurf conservation grades of the two nodes involved in a link.

Index Node1 Node2 Recurrence Int. Strength Hub1? Hub2? Community ConSurf1 ConSurf2
1L:L:?2 L:L:Y1 37.151817.89YesYes100
2L:L:Y1 R:R:Y129 40.23067.94YesNo005
3L:L:Y1 R:R:M132 89.37228.38YesYes108
4L:L:Y1 R:R:V281 11.49646.31YesNo006
5R:R:I183 R:R:Y129 39.559814.51NoNo045
6R:R:I183 R:R:L200 39.02325.71NoNo044
7R:R:L125 R:R:L200 34.18684.15NoNo054
8L:L:F4 R:R:L125 32.747415.83YesNo005
9L:L:?2 R:R:I304 34.12318.71YesYes105
10R:R:I304 R:R:Y56 24.3489.67YesYes157
11R:R:L102 R:R:Y56 16.93765.86NoYes077
12R:R:L102 R:R:Y308 12.003514.07NoYes077
13L:L:F4 R:R:W114 22.04015.01YesYes308
14L:L:F4 R:R:C198 13.91355.59YesNo309
15R:R:A298 R:R:I52 12.16031.62NoYes015
16R:R:A298 R:R:L48 10.51644.73NoNo012
17R:R:M132 R:R:W274 91.96215.82YesYes188
18R:R:N310 R:R:W274 97.664812.43YesYes098
19R:R:N310 R:R:N314 1008.17YesYes099
20R:R:L91 R:R:N314 47.809210.98YesYes299
21R:R:L91 R:R:Y318 50.64694.69YesYes299
22R:R:M142 R:R:Y318 61.1619.58YesYes299
23R:R:I88 R:R:M142 28.10894.37NoYes089
24R:R:F325 R:R:I88 26.9725.02YesNo088
25R:R:L139 R:R:N314 47.42496.87NoYes289
26R:R:L139 R:R:Y318 47.24764.69NoYes289
27R:R:M142 R:R:Y87 41.51755.99YesYes297
28R:R:N169 R:R:Y87 29.12539.3NoYes077
29R:R:I86 R:R:N169 10.53234.25YesNo067
30R:R:N169 R:R:N90 18.624813.62NoNo079
31R:R:N90 R:R:W173 17.49475.65NoYes099
32R:R:C121 R:R:W114 13.36775.22NoYes398
33R:R:C121 R:R:C198 13.04947.28NoNo399
34R:R:C121 R:R:T189 24.56173.38NoNo094
35R:R:E118 R:R:T189 17.08548.47NoNo044
36R:R:Y233 R:R:Y318 45.90154.96YesYes289
37R:R:S143 R:R:Y233 19.74588.9NoYes098
38R:R:C232 R:R:S143 12.63785.16NoNo089
39R:R:C232 R:R:Y147 11.53736.72NoYes088
40R:R:M236 R:R:Y233 27.87243.59NoYes288
41R:R:L240 R:R:M236 23.06784.24NoNo288
42R:R:D210 R:R:K214 10.61649.68NoYes045
43R:R:E118 R:R:V188 15.2052.85NoNo044
44R:R:R190 R:R:V188 11.416817YesNo734
45R:R:H278 R:R:W274 11.10538.46NoYes178
46R:R:L240 R:R:V243 21.944.47NoNo086
47R:R:L245 R:R:V243 20.87134.47NoNo036
48R:R:K252 R:R:L245 11.07571.41YesNo023
49R:R:E251 R:R:L246 12.35592.65NoNo032
50R:R:K214 R:R:V281 10.8377.59YesNo056
51R:R:F202 R:R:L200 10.44137.31YesNo064
Download PSN data

2D representation of the global metapath, ligand(s) interactions and
histograms of path distribution according to several parameters
(click on the image to enlarge it 🔍):

A 2D representation of the global communication in the network.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

Number of shortest communication paths as a function of the average residue correlation.

Number of shortest communication paths as a function of the average interaction strength of their links.

Number of shortest communication paths as a function of the % of hub nodes in each path.

Number of shortest communication paths as a function of the number of nodes in each path.

Number of shortest communication paths as a function of the % of correlated nodes in each path.


2D representation of the interactions of this orthosteric/allosteric ligand.


Links and nodes colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
L:L:Y1 R:R:Y129 7.94 1 Yes No 0 5 0 1
L:L:Y1 R:R:M132 8.38 1 Yes Yes 0 8 0 1
L:L:Y1 R:R:V217 7.57 1 Yes No 0 5 0 1
L:L:Y1 R:R:I277 3.63 1 Yes No 0 5 0 1
L:L:Y1 R:R:V281 6.31 1 Yes No 0 6 0 1
L:L:?2 R:R:I277 4.36 1 Yes No 0 5 0 1
L:L:?2 R:R:I304 8.71 1 Yes Yes 0 5 0 1
L:L:F4 R:R:Q105 5.86 3 Yes Yes 0 5 0 1
L:L:F4 R:R:K108 6.2 3 Yes No 0 4 0 1
L:L:F4 R:R:W114 5.01 3 Yes Yes 0 8 0 1
L:L:F4 R:R:L125 15.83 3 Yes No 0 5 0 1
L:L:F4 R:R:D128 5.97 3 Yes No 0 5 0 1
L:L:F4 R:R:C198 5.59 3 Yes No 0 9 0 1
L:L:?5 R:R:K214 7.37 0 No Yes 0 5 0 1
L:L:?5 R:R:W284 19.83 0 No No 0 4 0 1
R:R:H301 R:R:Y56 13.07 1 Yes Yes 4 7 2 2
R:R:I304 R:R:Y56 9.67 1 Yes Yes 5 7 1 2
R:R:Q105 R:R:T101 4.25 3 Yes No 5 7 1 2
R:R:T101 R:R:Y308 4.99 3 No Yes 7 7 2 2
R:R:D128 R:R:Q105 6.53 3 No Yes 5 5 1 1
R:R:Q105 R:R:Y308 11.27 3 Yes Yes 5 7 1 2
R:R:K108 R:R:W114 5.8 3 No Yes 4 8 1 1
R:R:F116 R:R:W114 20.04 0 Yes Yes 7 8 2 1
R:R:C121 R:R:W114 5.22 3 No Yes 9 8 2 1
R:R:V124 R:R:W114 4.9 0 No Yes 5 8 2 1
R:R:C198 R:R:W114 13.06 3 No Yes 9 8 1 1
R:R:C121 R:R:C198 7.28 3 No No 9 9 2 1
R:R:L125 R:R:L200 4.15 0 No No 5 4 1 2
R:R:D128 R:R:Y308 8.05 3 No Yes 5 7 1 2
R:R:I183 R:R:Y129 14.51 0 No No 4 5 2 1
R:R:F133 R:R:M132 3.73 0 Yes Yes 7 8 2 1
R:R:M132 R:R:V217 4.56 1 Yes No 8 5 1 1
R:R:M132 R:R:W274 5.82 1 Yes Yes 8 8 1 2
R:R:I183 R:R:L200 5.71 0 No No 4 4 2 2
R:R:D210 R:R:K214 9.68 0 No Yes 4 5 2 1
R:R:K214 R:R:V281 7.59 0 Yes No 5 6 1 1
R:R:I289 R:R:W284 5.87 4 Yes No 1 4 2 1
R:R:R291 R:R:W284 27.99 4 No No 1 4 2 1
R:R:I289 R:R:R291 3.76 4 Yes No 1 1 2 2
R:R:I304 R:R:L300 7.14 1 Yes No 5 5 1 2
R:R:H301 R:R:I304 3.98 1 Yes Yes 4 5 2 1
R:R:C303 R:R:I277 3.27 0 No No 6 5 2 1
R:R:A187 R:R:L125 3.15 0 No No 4 5 2 1
R:R:K214 R:R:T285 3 0 Yes No 5 4 1 2
R:R:G117 R:R:W114 2.81 0 No Yes 7 8 2 1

Location and physicochemical properties of the interaction partners of this ligand

Interactions of this ligand

Similarities between the interactions of this ligand and those of other networks

PDB Summary
PDB 9YDP_nogp
Class
SubFamily
Type
SubType
Species
Ligand
Other Ligand(s)
Protein Partners
PDB Resolution
Date
D.O.I.
Net Summary
Imin 3.59
Number of Linked Nodes 275
Number of Links 306
Number of Hubs 41
Number of Links mediated by Hubs 163
Number of Communities 9
Number of Nodes involved in Communities 58
Number of Links involved in Communities 77
Path Summary
Number Of Nodes in MetaPath 52
Number Of Links MetaPath 51
Number of Shortest Paths 70254
Length Of Smallest Path 3
Average Path Length 14.9066
Length of Longest Path 31
Minimum Path Strength 1.31
Average Path Strength 7.30765
Maximum Path Strength 23.91
Minimum Path Correlation 0.7
Average Path Correlation 0.929045
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 4.54545
Average % Of Corr. Nodes 47.0619
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 51.6947
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process
Gene OntologyCellular Component
SCOP2Domain Identifier• G protein-coupled receptor-like   • Transducin (heterotrimeric G protein), gamma chain
SCOP2Family Identifier• G protein-coupled receptor-like   • Transducin (heterotrimeric G protein), gamma chain
Membrane Protein Annotations-• Orientations of Proteins in Membranes database (OPM)   • Protein Data Bank of Transmembrane Proteins (PDBTM)   • MemProtMD


Details about the values in these tables can be found in the corresponding documentation page .
CodeDAL
PDB ResiduesL:L:?2
Environment DetailsOpen EMBL-EBI Page
CodeDAL
NameD-Alanine
SynonymsD-Alanine
Identifier
FormulaC3 H7 N O2
Molecular Weight89.093
SMILES
PubChem71080
Formal Charge0
Total Atoms13
Total Chiral Atoms1
Total Bonds12
Total Aromatic Bonds0

CodeDLE
PDB ResiduesL:L:?5
Environment DetailsOpen EMBL-EBI Page
CodeDLE
NameD-Leucine
Synonyms(R)-leucine
Identifier
FormulaC6 H13 N O2
Molecular Weight131.173
SMILES
PubChem6950207
Formal Charge0
Total Atoms22
Total Chiral Atoms1
Total Bonds21
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP41143
Sequence
>9YDP_nogp_Chain_R
SASSLALAI AITALYSAV CAVGLLGNV LVMFGIVRY TKMKTATNI 
YIFNLALAD ALATSTLPF QSAKYLMET WPFGELLCK AVLSIDYYN 
MFTSIFTLT MMSVDRYIA VCHPVKALD FRTPAKAKL INICIWVLA 
SGVGVPIMV MAVTRPRDG AVVCMLQFP SPSWYWDTV TKICVFLFA 
FVVPILIIT VCYGLMLLR LRSVRLLSG SKEKDRSLR RITRMVLVV 
VGAFVVCWA PIHIFVIVW TLVDIDRRD PLVVAALHL CIALGYANS 
SLNPVLYAF LDENFKRCF RQLCR


Click on each residue to open a popup with some information about it.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  




This receptor, from the same or other species and bound to the same or other ligands, is also present in the following networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
4EJ4APeptideOpioidδMus musculusNaltrindole--3.42012-05-16doi.org/10.1038/nature11111
4N6HAPeptideOpioidδHomo sapiensNaltrindoleNa-1.82013-12-25doi.org/10.1038/nature12944
4RWAAPeptideOpioidδHomo sapiensDIPP-NH2--3.282015-01-14doi.org/10.1038/nsmb.2965
4RWDAPeptideOpioidδHomo sapiensDIPP-NH2Na-2.72015-01-14doi.org/10.1038/nsmb.2965
6PT2APeptideOpioidδHomo sapiensKGCHM07--2.82019-12-11doi.org/10.1126/sciadv.aax9115
6PT3APeptideOpioidδHomo sapiensDPI-287--3.32019-12-11doi.org/10.1126/sciadv.aax9115
8F7SAPeptideOpioidδHomo sapiensDeltorphin-Gi1/β1/γ232022-12-14doi.org/10.1016/j.cell.2022.12.026
8F7S (No Gprot) APeptideOpioidδHomo sapiensDeltorphin-32022-12-14doi.org/10.1016/j.cell.2022.12.026
8Y45APeptideOpioidδHomo sapiensADL5859-Gi2/β1/γ23.452024-11-27doi.org/10.1038/s41467-024-52601-1
8Y45 (No Gprot) APeptideOpioidδHomo sapiensADL5859-3.452024-11-27doi.org/10.1038/s41467-024-52601-1
9CGJAPeptideOpioidδHomo sapiensC6-Quino-Gi1/β1/γ22.82025-04-02doi.org/10.1038/s41467-025-57734-5
9CGJ (No Gprot) APeptideOpioidδHomo sapiensC6-Quino-2.82025-04-02doi.org/10.1038/s41467-025-57734-5
9CGKAPeptideOpioidδHomo sapiensC5-Quino-Gi1/β1/γ22.622025-04-02doi.org/10.1038/s41467-025-57734-5
9CGK (No Gprot) APeptideOpioidδHomo sapiensC5-Quino-2.622025-04-02doi.org/10.1038/s41467-025-57734-5
9YDPAPeptideOpioidδHomo sapiensDADLE-chim(NtGi1L-Gs-CtGi1)/β1/γ21.952025-12-1010.1101/2025.10.16.682975
9YDP (No Gprot) APeptideOpioidδHomo sapiensDADLE-1.952025-12-1010.1101/2025.10.16.682975
9YDQAPeptideOpioidδHomo sapiensDADLEMIPS3614chim(NtGi1L-Gs-CtGi1)/β1/γ21.942025-12-1010.1101/2025.10.16.682975
9YDQ (No Gprot) APeptideOpioidδHomo sapiensDADLEMIPS36141.942025-12-1010.1101/2025.10.16.682975
9YDRAPeptideOpioidδHomo sapiensDADLEMIPS3983chim(NtGi1L-Gs-CtGi1)/β1/γ22.142025-12-1010.1101/2025.10.16.682975
9YDR (No Gprot) APeptideOpioidδHomo sapiensDADLEMIPS39832.142025-12-1010.1101/2025.10.16.682975
8Y71APeptideOpioidδHomo sapiensA1D6FBMS986187Gi1/β1/γ22.972026-01-07To be published
8Y71 (No Gprot) APeptideOpioidδHomo sapiensA1D6FBMS9861872.972026-01-07To be published




You can download a compressed (zip) file with structure(s), 3D outputs (as PyMol and VMD scripts) and numerical data files (as csv and plain text files).

Download 9YDP_nogp.zip



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