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:Y45 6.338517
2R:R:I53 6.3625445
3R:R:M72 5.8075406
4R:R:Y76 5.4775407
5R:R:H79 6.305469
6R:R:D84 7.6425419
7R:R:F87 7.282517
8R:R:L91 4.2425418
9R:R:W94 7.40286717
10R:R:W102 7.87571719
11R:R:F104 10.8125417
12R:R:L108 2.225415
13R:R:H113 7.145416
14R:R:Y116 8.88416
15R:R:T117 5.8525415
16R:R:Y121 6.17286717
17R:R:F129 6.44405
18R:R:R134 5.575409
19R:R:Y135 7.3275478
20R:R:I138 4.03408
21R:R:R148 8.1625406
22R:R:W161 4.3925409
23R:R:Y190 9.842514
24R:R:L194 6.4502
25R:R:W195 10.1467615
26R:R:Y219 4.478508
27R:R:F248 7.20667619
28R:R:W252 9.15619
29R:R:Y255 7.6625407
30R:R:I259 5.4775405
31R:R:E288 7.17515
32R:R:F292 7.79417
33R:R:H294 7.23619
34R:R:N298 8.46409
35R:R:Y302 12.0575459
36S:S:Y45 6.165427
37S:S:M63 4.715496
38S:S:M72 6.67254106
39S:S:H79 6.90254129
40S:S:D84 6.118539
41S:S:F87 8.55507
42S:S:W94 8.56167627
43S:S:W102 6.77729
44S:S:H113 7.0725426
45S:S:Y116 8.124526
46S:S:Y121 8.6925147
47S:S:F129 4.7785115
48S:S:R134 4.6325409
49S:S:Y135 7.64254158
50S:S:R148 7.765106
51S:S:W161 4.9825409
52S:S:F174 8.6275424
53S:S:R183 6.17423
54S:S:Y190 9.636524
55S:S:L194 5.63402
56S:S:W195 10.36625
57S:S:F199 5.988525
58S:S:M205 3.87404
59S:S:F248 7.56667639
60S:S:W252 8.86667639
61S:S:Y255 8.1425407
62S:S:I259 5.9525405
63S:S:V280 4.38254165
64S:S:E288 7.618525
65S:S:F292 6.9825427
66S:S:H294 6.305639
67S:S:N298 7.452589
68S:S:Y302 10.368589
69W:W:?1 9.61889910
70K:K:?1 10.12820
   

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:I259 R:R:Y255 10.311213.3YesYes057
2R:R:E288 R:R:Y255 40.56225.61YesYes057
3R:R:E288 W:W:?1 37.008611.02YesYes150
4R:R:W94 R:R:Y45 13.22739.65YesYes177
5R:R:L41 R:R:Y45 15.430510.55NoYes067
6R:R:L41 R:R:N37 13.74035.49NoNo063
7R:R:W252 R:R:Y255 33.78096.75YesYes097
8R:R:H294 R:R:W252 13.815113.75YesYes199
9R:R:C295 R:R:H294 17.11158.85NoYes199
10R:R:C295 R:R:V88 22.06513.42NoNo096
11R:R:I53 R:R:V88 13.286.14YesNo056
12R:R:D84 R:R:N56 14.42055.39YesNo099
13R:R:F248 R:R:W252 47.21289.02YesYes199
14R:R:F248 R:R:L127 47.55338.53YesNo098
15R:R:N298 R:R:R77 10.132513.26YesNo098
16R:R:I245 R:R:L127 43.57224.28NoNo078
17R:R:I245 R:R:Y219 42.80583.63NoYes078
18R:R:T241 R:R:Y219 32.58474.99NoYes078
19R:R:R134 R:R:T241 31.01367.76YesNo097
20R:R:A137 R:R:R134 28.74864.15NoYes089
21R:R:A137 R:R:R148 27.95326.91NoYes086
22R:R:D133 R:R:R148 19.102414.29NoYes086
23R:R:D133 R:R:M72 18.28868.32NoYes086
24R:R:A152 R:R:M72 12.54944.83NoYes036
25R:R:A152 R:R:Y76 11.72344NoYes037
26R:R:H294 R:R:N119 11.79833.83YesNo198
27R:R:F87 R:R:W94 26.35244.01YesYes177
28R:R:H113 W:W:?1 1003.89YesYes160
29R:R:H113 R:R:R188 96.860211.28YesNo165
30R:R:L120 R:R:W252 29.6675.69NoYes079
31R:R:R188 R:R:Y190 99.70088.23NoYes154
32R:R:W195 R:R:Y190 96.694510.61YesYes154
33R:R:N192 R:R:W195 98.87635.65NoYes015
34R:R:L194 R:R:N192 98.69088.24YesNo021
35R:R:D193 R:R:L194 98.42215.43NoYes012
36R:R:D193 S:S:L194 98.35115.43NoYes012
37S:S:L194 S:S:N192 98.12895.49YesNo021
38S:S:N192 S:S:W195 97.8935.65NoYes015
39S:S:W195 S:S:Y190 95.728810.61YesYes254
40S:S:R188 S:S:Y190 96.910510.29NoYes254
41S:S:H113 S:S:R188 93.552411.28YesNo265
42K:K:?1 S:S:H113 95.51124.86YesYes206
43K:K:?1 S:S:E288 27.861611.02YesYes205
44S:S:E288 S:S:Y255 29.66628.98YesYes057
45S:S:I259 S:S:Y255 15.641910.88YesYes057
46K:K:?1 S:S:Y116 53.1917.97YesYes206
47S:S:F87 S:S:Y116 38.69034.13YesYes076
48S:S:F87 S:S:N119 40.38215.71YesNo078
49S:S:D84 S:S:N119 34.18865.39YesNo398
50S:S:D84 S:S:L80 35.40095.43YesNo099
51S:S:L80 S:S:N298 35.01536.87NoYes099
52S:S:N298 S:S:Y302 34.01154.65YesYes899
53S:S:D74 S:S:Y302 33.49168.05NoYes089
54S:S:D74 S:S:M63 31.04575.54NoYes086
55S:S:M63 S:S:R70 29.33656.2YesNo966
56S:S:K75 S:S:R70 28.96554.95NoNo066
57S:S:K75 S:S:M72 27.27387.2NoYes066
58S:S:A152 S:S:M72 17.99174.83NoYes036
59S:S:A152 S:S:Y76 17.53295.34NoNo037
60S:S:F129 S:S:Y76 16.61078.25YesNo057
61S:S:F129 S:S:V160 11.90825.24YesNo057
62S:S:V156 S:S:V160 11.42953.21NoNo057
63S:S:H79 S:S:V156 10.45169.69YesNo1295
64S:S:L120 S:S:Y116 15.001514.07NoYes076
65S:S:L120 S:S:W252 14.7354.56NoYes079
66S:S:H294 S:S:W252 13.383810.58YesYes399
67S:S:W252 S:S:Y255 18.56347.72YesYes097
68K:K:?1 S:S:D97 10.625722.56YesNo205
69S:S:D97 S:S:W102 10.18836.7NoYes259
70S:S:F248 S:S:W252 16.992410.02YesYes399
71S:S:F248 S:S:L127 12.77089.74YesNo098
72S:S:C251 S:S:H294 12.28992.95NoYes089
73R:R:W94 W:W:?1 32.999216.35YesYes170
74R:R:D84 R:R:N119 19.2076.73YesNo198
75R:R:F87 R:R:N119 31.248812.08YesNo178
76R:R:L120 R:R:Y116 29.877711.72NoYes076
77R:R:Y116 W:W:?1 28.681512.4YesYes160
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:W94 S:S:Y45 9.65 2 Yes Yes 7 7 1 2
S:S:F292 S:S:Y45 4.13 2 Yes Yes 7 7 2 2
S:S:F87 S:S:L91 8.53 0 Yes No 7 8 2 2
S:S:F87 S:S:Y116 4.13 0 Yes Yes 7 6 2 1
S:S:F292 S:S:F87 11.79 2 Yes Yes 7 7 2 2
S:S:L91 S:S:W94 5.69 0 No Yes 8 7 2 1
S:S:W94 S:S:Y116 7.72 2 Yes Yes 7 6 1 1
S:S:E288 S:S:W94 4.36 2 Yes Yes 5 7 1 1
S:S:F292 S:S:W94 5.01 2 Yes Yes 7 7 2 1
K:K:?1 S:S:W94 18.94 2 Yes Yes 0 7 0 1
S:S:D97 S:S:W102 6.7 2 No Yes 5 9 1 2
S:S:D97 S:S:R183 4.76 2 No Yes 5 3 1 1
K:K:?1 S:S:D97 22.56 2 Yes No 0 5 0 1
S:S:N101 S:S:R183 7.23 0 No Yes 4 3 2 1
S:S:D171 S:S:H113 6.3 2 No Yes 4 6 2 1
S:S:A175 S:S:H113 5.85 0 No Yes 4 6 2 1
S:S:H113 S:S:R188 11.28 2 Yes No 6 5 1 2
K:K:?1 S:S:H113 4.86 2 Yes Yes 0 6 0 1
S:S:L120 S:S:Y116 14.07 0 No Yes 7 6 2 1
S:S:E288 S:S:Y116 6.73 2 Yes Yes 5 6 1 1
K:K:?1 S:S:Y116 7.97 2 Yes Yes 0 6 0 1
S:S:D171 S:S:R188 8.34 2 No No 4 5 2 2
S:S:I185 S:S:R183 6.26 0 No Yes 3 3 2 1
K:K:?1 S:S:R183 6.43 2 Yes Yes 0 3 0 1
K:K:?1 S:S:D187 7.18 2 Yes No 0 3 0 1
S:S:E288 S:S:Y255 8.98 2 Yes Yes 5 7 1 2
S:S:E288 S:S:F292 7 2 Yes Yes 5 7 1 2
K:K:?1 S:S:E288 11.02 2 Yes Yes 0 5 0 1
S:S:D187 S:S:F189 3.58 0 No No 3 3 1 2
S:S:E32 S:S:R30 3.49 0 No No 4 5 1 2
K:K:?1 S:S:E32 2 2 Yes No 0 4 0 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:E32 W:W:?1 5.01 0 No Yes 4 0 1 0
R:R:L91 R:R:Y45 4.69 1 Yes Yes 8 7 2 2
R:R:W94 R:R:Y45 9.65 1 Yes Yes 7 7 1 2
R:R:F292 R:R:Y45 4.13 1 Yes Yes 7 7 2 2
R:R:F87 R:R:L91 4.87 1 Yes Yes 7 8 2 2
R:R:F87 R:R:W94 4.01 1 Yes Yes 7 7 2 1
R:R:F292 R:R:F87 12.86 1 Yes Yes 7 7 2 2
R:R:L91 R:R:W94 4.56 1 Yes Yes 8 7 2 1
R:R:W94 R:R:Y116 5.79 1 Yes Yes 7 6 1 1
R:R:E288 R:R:W94 5.45 1 Yes Yes 5 7 1 1
R:R:F292 R:R:W94 6.01 1 Yes Yes 7 7 2 1
R:R:W94 W:W:?1 16.35 1 Yes Yes 7 0 1 0
R:R:D97 R:R:W102 5.58 0 No Yes 5 9 1 2
R:R:D97 W:W:?1 19.49 0 No Yes 5 0 1 0
R:R:N101 R:R:R183 4.82 0 No No 4 3 2 1
R:R:C109 R:R:W102 3.92 1 No Yes 9 9 2 2
R:R:C186 R:R:W102 16.98 1 No Yes 9 9 1 2
R:R:C109 R:R:C186 7.28 1 No No 9 9 2 1
R:R:D171 R:R:H113 7.56 1 No Yes 4 6 2 1
R:R:A175 R:R:H113 5.85 0 No Yes 4 6 2 1
R:R:H113 R:R:R188 11.28 1 Yes No 6 5 1 2
R:R:H113 W:W:?1 3.89 1 Yes Yes 6 0 1 0
R:R:L120 R:R:Y116 11.72 0 No Yes 7 6 2 1
R:R:E288 R:R:Y116 5.61 1 Yes Yes 5 6 1 1
R:R:Y116 W:W:?1 12.4 1 Yes Yes 6 0 1 0
R:R:D171 R:R:R188 8.34 1 No No 4 5 2 2
R:R:I185 R:R:R183 6.26 0 No No 3 3 2 1
R:R:R183 W:W:?1 6.43 0 No Yes 3 0 1 0
R:R:C186 W:W:?1 4.8 1 No Yes 9 0 1 0
R:R:D187 R:R:F189 4.78 0 No No 3 3 1 2
R:R:D187 W:W:?1 7.18 0 No Yes 3 0 1 0
R:R:E288 R:R:Y255 5.61 1 Yes Yes 5 7 1 2
R:R:E288 R:R:F292 8.16 1 Yes Yes 5 7 1 2
R:R:E288 W:W:?1 11.02 1 Yes Yes 5 0 1 0
R:R:E32 R:R:R30 3.49 0 No No 4 5 1 2

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 3ODU_poly
Class A
SubFamily Protein
Type Chemokine
SubType CXCR4
Species Homo sapiens
Ligand -
Other Ligand(s) IT1t
Protein Partners -
PDB Resolution 2.5
Date 2010-10-27
D.O.I. 10.1126/science.1194396
Net Summary
Imin 3.63
Number of Linked Nodes 551
Number of Links 601
Number of Hubs 70
Number of Links mediated by Hubs 277
Number of Communities 17
Number of Nodes involved in Communities 102
Number of Links involved in Communities 132
Path Summary
Number Of Nodes in MetaPath 78
Number Of Links MetaPath 77
Number of Shortest Paths 231879
Length Of Smallest Path 3
Average Path Length 22.7582
Length of Longest Path 60
Minimum Path Strength 1.38
Average Path Strength 7.30339
Maximum Path Strength 22.58
Minimum Path Correlation 0.77
Average Path Correlation 0.985202
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 4
Average % Of Corr. Nodes 70.1615
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 51.6697
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
>3ODU_poly_Chain_R
PCFREENAN FNKIFLPTI YSIIFLTGI VGNGLVILV MGYQKKLRS 
MTDKYRLHL SVADLLFVI TLPFWAVDA VANWYFGNF LCKAVHVIY 
TVNLYSSVW ILAFISLDR YLAIVHATN SQRPRKLLA EKVVYVGVW 
IPALLLTIP DFIFANVSE ADDRYICDR FYPNDLWVV VFQFQHIMV 
GLILPGIVI LSCYCIIIS KLSHSKGHQ KRKALKTTV ILILAFFAC 
WLPYYIGIS IDSFILLEI IKQGCEFEN TVHKWISIT EALAFFHCC 
LNPILYAFL GAKFKTSAQ HALTS


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 3ODU_poly.zip



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