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
1R:R:N37 8.4875473
2R:R:Y45 6.834537
3R:R:Y76 5.094557
4R:R:D84 7.445409
5R:R:F93 7.75446
6R:R:W94 12.79537
7R:R:W102 10.166549
8R:R:F104 12.725447
9R:R:Y116 7.61333636
10R:R:F129 4.87655
11R:R:D133 8.135458
12R:R:R134 5.9409
13R:R:Y135 6.0575468
14R:R:H140 7.9075466
15R:R:R148 7.3175456
16R:R:F174 6.065494
17R:R:R183 3.52403
18R:R:R188 7.6575435
19R:R:Y190 8.875404
20R:R:W195 7.74695
21R:R:F199 6.07405
22R:R:H203 4.5575404
23R:R:Y219 5.5575488
24R:R:F248 7.3445119
25R:R:W252 9.395119
26R:R:Y255 7.6025407
27R:R:L267 6.6175411
28R:R:I286 3.574576
29R:R:E288 7.572535
30R:R:F292 7.776537
31R:R:H294 7.5054119
32R:R:P299 5.17409
33S:S:Y45 6.966517
34S:S:I53 3.215405
35S:S:I60 3.0275407
36S:S:M72 5.7325426
37S:S:Y76 5.65627
38S:S:R77 9.3175408
39S:S:D84 6.725409
40S:S:F87 9.18333617
41S:S:W94 8.66714717
42S:S:W102 9.682519
43S:S:Y116 9.15333616
44S:S:W125 5.974505
45S:S:F129 5.526525
46S:S:D133 8.53428
47S:S:R134 5.92333629
48S:S:Y135 6.644568
49S:S:H140 8.24466
50S:S:R148 8.5975426
51S:S:L151 5.81424
52S:S:V156 6.59425
53S:S:F174 7.935414
54S:S:R183 5.492513
55S:S:R188 7.4175415
56S:S:Y190 7.302514
57S:S:L194 4.9425402
58S:S:W195 8.38286715
59S:S:F199 7.4825415
60S:S:F248 6.713336109
61S:S:W252 8.7285109
62S:S:Y255 6.94507
63S:S:T287 3.785406
64S:S:F292 7.7275417
65S:S:H294 7.128336109
66S:S:P299 6.3775409
67W:W:?1 11.1688830
68K:K:?1 9910
   

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
1R:R:L41 R:R:Y45 15.01718.21NoYes067
2R:R:W94 R:R:Y45 25.458914.47YesYes377
3R:R:D84 R:R:N119 14.16046.73YesNo098
4R:R:F87 R:R:N119 14.76715.71NoNo078
5R:R:D133 R:R:Y76 20.79045.75YesYes587
6R:R:F129 R:R:Y76 20.26266.19YesYes557
7R:R:F129 R:R:V160 20.23117.87YesNo057
8R:R:V160 R:R:W125 20.24433.68NoNo075
9R:R:P211 R:R:W125 20.325624.32NoNo095
10R:R:P211 R:R:V124 20.38797.07NoNo097
11R:R:F248 R:R:V124 20.56813.93YesNo097
12R:R:F248 R:R:W252 22.225410.02YesYes1199
13R:R:W252 R:R:Y255 28.55767.72YesYes097
14R:R:E288 R:R:Y255 34.31525.61YesYes057
15R:R:D133 R:R:R148 20.272613.1YesYes586
16R:R:F104 R:R:W102 10.03820.04YesYes479
17R:R:D97 R:R:W102 16.62974.47NoYes059
18R:R:D97 W:W:?1 17.44827.69NoYes050
19R:R:W94 W:W:?1 23.158423.24YesYes370
20R:R:R188 W:W:?1 86.97484.59YesYes350
21R:R:F248 R:R:L127 10.7827.31YesNo098
22R:R:L136 R:R:R148 21.5354.86NoYes056
23R:R:L136 R:R:Y135 21.5693.52NoYes058
24R:R:F199 R:R:Y190 46.59656.19YesYes054
25R:R:R188 R:R:Y190 91.21313.38YesYes054
26R:R:F174 R:R:Y190 45.724613.41YesYes044
27R:R:F174 R:R:W195 45.66414.01YesYes945
28R:R:F199 R:R:W195 48.5825.01YesYes055
29R:R:W195 S:S:L267 95.07266.83YesNo051
30S:S:L266 S:S:L267 99.54641.38NoNo031
31R:R:L194 S:S:L266 99.62391.38NoNo023
32R:R:L194 S:S:V197 99.74051.49NoNo023
33R:R:V197 S:S:V197 99.86083.21NoNo033
34R:R:V197 S:S:L194 1005.96NoYes032
35R:R:L267 S:S:L194 51.02625.54YesYes012
36R:R:L267 S:S:W195 49.137613.67YesYes115
37S:S:L194 S:S:N192 49.48534.12YesNo021
38S:S:N192 S:S:W195 49.35379.04NoYes015
39S:S:W195 S:S:Y190 92.02563.86YesYes154
40S:S:R188 S:S:Y190 93.234512.35YesYes154
41K:K:?1 S:S:R188 89.88954.59YesYes105
42K:K:?1 S:S:W94 31.064713.77YesYes107
43K:K:?1 S:S:E288 26.645114.02YesNo105
44S:S:E288 S:S:Y255 27.310312.35NoYes057
45K:K:?1 S:S:Y116 23.6854.43YesYes106
46S:S:F87 S:S:W94 19.74356.01YesYes177
47S:S:F87 S:S:N119 40.639115.71YesNo078
48S:S:D84 S:S:N119 28.68044.04YesNo098
49S:S:C295 S:S:V88 15.63693.42NoNo096
50S:S:I53 S:S:V88 11.73514.61YesNo056
51S:S:F87 S:S:Y116 19.30068.25YesYes176
52S:S:H294 S:S:N119 15.99357.65YesNo098
53S:S:C295 S:S:H294 13.27847.37NoYes099
54S:S:W252 S:S:Y255 20.20467.72YesYes097
55S:S:D84 S:S:N56 17.33786.73YesNo099
56R:R:I221 R:R:Y135 13.69112.42NoYes048
57R:R:I221 R:R:S217 13.64511.55NoNo043
58R:R:I213 R:R:S217 13.63121.55NoNo033
59R:R:I213 S:S:L210 13.64072.85NoNo036
60S:S:L210 S:S:W125 13.68922.28NoYes065
61S:S:V160 S:S:W125 10.19553.68NoYes075
62S:S:F248 S:S:W252 13.08259.02YesYes1099
63K:K:?1 S:S:C186 11.19713.6YesNo109
64S:S:P211 S:S:W125 20.143517.57NoYes095
65S:S:P211 S:S:V124 20.18388.84NoNo097
66S:S:F248 S:S:V124 20.40875.24YesNo097
67R:R:F87 R:R:Y116 14.78788.25NoYes376
68R:R:Y116 W:W:?1 19.94074.43YesYes360
69R:R:E288 W:W:?1 27.177412.02YesYes350
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
S:S:L91 S:S:Y45 3.52 1 No Yes 8 7 2 2
S:S:W94 S:S:Y45 11.58 1 Yes Yes 7 7 1 2
S:S:F87 S:S:T90 3.89 1 Yes No 7 6 2 2
S:S:F87 S:S:L91 7.31 1 Yes No 7 8 2 2
S:S:F87 S:S:W94 6.01 1 Yes Yes 7 7 2 1
S:S:F87 S:S:Y116 8.25 1 Yes Yes 7 6 2 1
S:S:F292 S:S:F87 13.93 1 Yes Yes 7 7 2 2
S:S:T90 S:S:W94 4.85 1 No Yes 6 7 2 1
S:S:L91 S:S:W94 6.83 1 No Yes 8 7 2 1
S:S:W94 S:S:Y116 10.61 1 Yes Yes 7 6 1 1
S:S:F292 S:S:W94 7.02 1 Yes Yes 7 7 2 1
K:K:?1 S:S:W94 13.77 1 Yes Yes 0 7 0 1
S:S:D97 S:S:R183 4.76 1 No Yes 5 3 1 1
K:K:?1 S:S:D97 20.51 1 Yes No 0 5 0 1
S:S:N101 S:S:R183 3.62 0 No Yes 4 3 2 1
S:S:C109 S:S:W102 3.92 1 No Yes 9 9 2 2
S:S:C186 S:S:W102 18.28 1 No Yes 9 9 1 2
S:S:C109 S:S:C186 7.28 1 No No 9 9 2 1
S:S:A175 S:S:H113 8.78 0 No No 4 6 2 1
S:S:H113 S:S:R188 6.77 1 No Yes 6 5 1 1
K:K:?1 S:S:H113 6.8 1 Yes No 0 6 0 1
S:S:L120 S:S:Y116 17.58 0 No Yes 7 6 2 1
S:S:E288 S:S:Y116 7.86 1 No Yes 5 6 1 1
S:S:F292 S:S:Y116 6.19 1 Yes Yes 7 6 2 1
K:K:?1 S:S:Y116 4.43 1 Yes Yes 0 6 0 1
S:S:D171 S:S:R188 5.96 0 No Yes 4 5 2 1
S:S:I185 S:S:R183 7.52 0 No Yes 3 3 2 1
K:K:?1 S:S:R183 9.18 1 Yes Yes 0 3 0 1
K:K:?1 S:S:C186 3.6 1 Yes No 0 9 0 1
S:S:D187 S:S:F189 8.36 0 No No 3 3 1 2
K:K:?1 S:S:D187 4.1 1 Yes No 0 3 0 1
S:S:R188 S:S:Y190 12.35 1 Yes Yes 5 4 1 2
K:K:?1 S:S:R188 4.59 1 Yes Yes 0 5 0 1
S:S:E288 S:S:Y255 12.35 1 No Yes 5 7 1 2
K:K:?1 S:S:E288 14.02 1 Yes No 0 5 0 1
S:S:D182 S:S:R183 2.38 0 No Yes 6 3 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

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
R:R:W94 R:R:Y45 14.47 3 Yes Yes 7 7 1 2
R:R:F292 R:R:Y45 4.13 3 Yes Yes 7 7 2 2
R:R:F87 R:R:Y116 8.25 3 No Yes 7 6 2 1
R:R:F292 R:R:F87 9.65 3 Yes No 7 7 2 2
R:R:W94 R:R:Y116 8.68 3 Yes Yes 7 6 1 1
R:R:E288 R:R:W94 6.54 3 Yes Yes 5 7 1 1
R:R:F292 R:R:W94 11.02 3 Yes Yes 7 7 2 1
R:R:W94 W:W:?1 23.24 3 Yes Yes 7 0 1 0
R:R:D97 R:R:W102 4.47 0 No Yes 5 9 1 2
R:R:D97 W:W:?1 27.69 0 No Yes 5 0 1 0
R:R:N101 R:R:R183 3.62 0 No Yes 4 3 2 1
R:R:A175 R:R:H113 5.85 0 No No 4 6 2 1
R:R:H113 R:R:R188 7.9 3 No Yes 6 5 1 1
R:R:H113 W:W:?1 7.77 3 No Yes 6 0 1 0
R:R:L120 R:R:Y116 8.21 0 No Yes 7 6 2 1
R:R:E288 R:R:Y116 7.86 3 Yes Yes 5 6 1 1
R:R:F292 R:R:Y116 8.25 3 Yes Yes 7 6 2 1
R:R:Y116 W:W:?1 4.43 3 Yes Yes 6 0 1 0
R:R:D171 R:R:R188 4.76 0 No Yes 4 5 2 1
R:R:I185 R:R:R183 3.76 0 No Yes 3 3 2 1
R:R:R183 W:W:?1 5.51 0 Yes Yes 3 0 1 0
R:R:D187 R:R:F189 7.17 0 No No 3 3 1 2
R:R:D187 W:W:?1 4.1 0 No Yes 3 0 1 0
R:R:R188 R:R:Y190 13.38 3 Yes Yes 5 4 1 2
R:R:R188 W:W:?1 4.59 3 Yes Yes 5 0 1 0
R:R:E288 R:R:Y255 5.61 3 Yes Yes 5 7 1 2
R:R:E288 R:R:F292 5.83 3 Yes Yes 5 7 1 2
R:R:E288 W:W:?1 12.02 3 Yes Yes 5 0 1 0
R:R:D181 R:R:R183 1.19 0 No Yes 2 3 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 3OE9_poly
Class A
SubFamily Protein
Type Chemokine
SubType CXCR4
Species Homo sapiens
Ligand -
Other Ligand(s) IT1t
Protein Partners -
PDB Resolution 3.1
Date 2010-10-27
D.O.I. 10.1126/science.1194396
Net Summary
Imin 3.52
Number of Linked Nodes 481
Number of Links 539
Number of Hubs 68
Number of Links mediated by Hubs 256
Number of Communities 13
Number of Nodes involved in Communities 94
Number of Links involved in Communities 131
Path Summary
Number Of Nodes in MetaPath 70
Number Of Links MetaPath 69
Number of Shortest Paths 269034
Length Of Smallest Path 3
Average Path Length 20.7195
Length of Longest Path 37
Minimum Path Strength 1.38
Average Path Strength 6.98347
Maximum Path Strength 25.465
Minimum Path Correlation 0.7
Average Path Correlation 0.956596
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 4
Average % Of Corr. Nodes 42.1312
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 51.611
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process
Gene OntologyCellular Component
SCOP2Domain Identifier
SCOP2Family Identifier
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 .
CodeITD
PDB ResiduesW:W:?1 K:K:?1
Environment DetailsOpen EMBL-EBI Page
CodeITD
Name(6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate
Synonyms
Identifier(6,6-dimethyl-5H-imidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylcarbamimidothioate
FormulaC21 H34 N4 S2
Molecular Weight406.651
SMILESCC1(CN2C(=CSC2=N1)CS/C(=N\C3CCCCC3)/NC4CCCCC4)C
PubChem25147749
Formal Charge0
Total Atoms61
Total Chiral Atoms0
Total Bonds64
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP61073
Sequence
>3OE9_poly_Chain_R
CFRNFNKIF LPTIYSIIF LTGIVGNGL VILVMGYQK KLRSMTDKY 
RLHLSVADL LFVITLPFW AVDAVANWY FGNFLCKAV HVIYTVNLY 
SSVWILAFI SLDRYLAIV HATNSQRPR KLLAEKVVY VGVWIPALL 
LTIPDFIFA NVSEADDRY ICDRFYPND LWVVVFQFQ HIMVGLILP 
GIVILSCYC IIISKLSHK ALKPTVILI LAFFACWLP YYIGISIDS 
FILLEIIKC EFENTVHKW ISITEALAF FHCCLNPIL YA


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
3ODUAProteinChemokineCXCR4Homo sapiens-IT1t-2.52010-10-2710.1126/science.1194396
3OE0AProteinChemokineCXCR4Homo sapiens-CVX15-2.92010-10-2710.1126/science.1194396
3OE6AProteinChemokineCXCR4Homo sapiens-IT1t-3.22010-10-2710.1126/science.1194396
3OE8AProteinChemokineCXCR4Homo sapiens-IT1t-3.12010-10-2710.1126/science.1194396
3OE9AProteinChemokineCXCR4Homo sapiens-IT1t-3.12010-10-2710.1126/science.1194396
4RWSAProteinChemokineCXCR4Homo sapiensvMIP-II--3.12015-02-1110.1126/science.1261064
8U4NAProteinChemokineCXCR4Homo sapiens-CholesterolGi1/&β;1/&γ;22.722024-03-1310.1101/2024.02.09.579708
8U4OAProteinChemokineCXCR4Homo sapiensCXCL12CholesterolGi1/&β;1/&γ;23.292024-03-1310.1101/2024.02.09.579708
8U4PAProteinChemokineCXCR4Homo sapiensAMD3100CholesterolGi1/&β;1/&γ;23.152024-03-1310.1101/2024.02.09.579708
8U4QAProteinChemokineCXCR4Homo sapiensREGN7663-FabCholesterolGi1/&β;1/&γ;23.362024-03-1310.1101/2024.02.09.579708
8U4RAProteinChemokineCXCR4Homo sapiensREGN7663-FabCholesterol-3.12024-03-1310.1101/2024.02.09.579708
3ODU (Dimer)AProteinChemokineCXCR4Homo sapiens-IT1t-2.52010-10-2710.1126/science.1194396
3OE8 (Dimer)AProteinChemokineCXCR4Homo sapiens-IT1t-3.12010-10-2710.1126/science.1194396
3OE9 (Dimer)AProteinChemokineCXCR4Homo sapiens-IT1t-3.12010-10-2710.1126/science.1194396




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 3OE9_poly.zip



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