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.

   

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.

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
R:R:R14 R:R:Y77 11.32 1 Yes Yes 4 6 2 1
R:R:F18 R:R:Y22 9.28 0 Yes Yes 5 8 2 1
R:R:F18 R:R:Y77 22.69 0 Yes Yes 5 6 2 1
R:R:F18 R:R:L279 7.31 0 Yes No 5 6 2 1
R:R:L70 R:R:Y22 7.03 0 No Yes 8 8 2 1
R:R:S283 R:R:Y22 11.45 0 No Yes 7 8 2 1
L:L:?1 R:R:Y22 5.98 1 Yes Yes 0 8 0 1
R:R:F66 R:R:L70 7.31 6 Yes No 7 8 2 2
R:R:F66 R:R:F97 7.5 6 Yes No 7 7 2 1
R:R:F66 R:R:S283 5.28 6 Yes No 7 7 2 2
R:R:W73 R:R:Y76 6.75 1 Yes Yes 7 6 1 2
R:R:C173 R:R:W73 6.53 1 Yes Yes 9 7 2 1
L:L:?1 R:R:W73 29.69 1 Yes Yes 0 7 0 1
R:R:Y76 R:R:Y77 10.92 1 Yes Yes 6 6 2 1
R:R:C173 R:R:Y76 5.38 1 Yes Yes 9 6 2 2
L:L:?1 R:R:Y77 8.64 1 Yes Yes 0 6 0 1
L:L:?1 R:R:F97 19.32 1 Yes No 0 7 0 1
R:R:F152 R:R:F98 9.65 1 No Yes 5 5 1 2
R:R:F152 R:R:F174 5.36 1 No Yes 5 4 1 1
L:L:?1 R:R:F152 13.11 1 Yes No 0 5 0 1
R:R:F174 R:R:S157 7.93 1 Yes Yes 4 5 1 2
L:L:?1 R:R:F174 9.66 1 Yes Yes 0 4 0 1
R:R:V184 R:R:Y177 6.31 0 No Yes 3 6 2 1
R:R:H188 R:R:Y177 5.44 1 Yes Yes 4 6 1 1
R:R:W255 R:R:Y177 5.79 1 Yes Yes 5 6 2 1
L:L:?1 R:R:Y177 11.29 1 Yes Yes 0 6 0 1
R:R:H188 R:R:Q252 7.42 1 Yes Yes 4 7 1 2
R:R:H188 R:R:T256 17.8 1 Yes No 4 5 1 2
L:L:?1 R:R:H188 13.11 1 Yes Yes 0 4 0 1
R:R:Q252 R:R:W255 6.57 0 Yes Yes 7 5 2 2
R:R:H275 R:R:W255 41.26 0 No Yes 5 5 2 2
R:R:H275 R:R:L279 10.29 0 No No 5 6 2 1
L:L:?1 R:R:L279 5.49 1 Yes No 0 6 0 1
R:R:A93 R:R:W73 3.89 0 No Yes 5 7 2 1
R:R:V21 R:R:Y22 3.79 0 No Yes 6 8 2 1
R:R:T69 R:R:W73 3.64 0 No Yes 6 7 2 1
R:R:F174 R:R:G94 3.01 1 Yes No 4 5 1 2
R:R:P19 R:R:Y77 2.78 0 No Yes 5 6 2 1
R:R:F174 R:R:L155 2.44 1 Yes 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 5ZKQ
Class A
SubFamily Lipid
Type Platelet-activating factor
SubType PAF
Species Homo sapiens
Ligand ABT-491
Other Ligand(s) -
Protein Partners -
PDB Resolution 2.9
Date 2018-06-20
D.O.I. 10.1038/s41594-018-0068-y
Net Summary
Imin 4.36
Number of Linked Nodes 266
Number of Links 306
Number of Hubs 47
Number of Links mediated by Hubs 164
Number of Communities 9
Number of Nodes involved in Communities 48
Number of Links involved in Communities 62
Path Summary
Number Of Nodes in MetaPath 64
Number Of Links MetaPath 63
Number of Shortest Paths 60076
Length Of Smallest Path 3
Average Path Length 13.6819
Length of Longest Path 37
Minimum Path Strength 1.425
Average Path Strength 8.5216
Maximum Path Strength 26.625
Minimum Path Correlation 0.7
Average Path Correlation 0.927171
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 3.44828
Average % Of Corr. Nodes 51.9901
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 55.0453
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 .
Code9EU
PDB ResiduesL:L:?1
Environment DetailsOpen EMBL-EBI Page
Code9EU
Name4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide
Synonyms
Identifier4-ethynyl-3-[3-fluoranyl-4-[(2-methylimidazo[4,5-c]pyridin-1-yl)methyl]phenyl]carbonyl-~{N},~{N}-dimethyl-indole-1-carboxamide
FormulaC28 H22 F N5 O2
Molecular Weight479.505
SMILESCc1nc2cnccc2n1Cc3ccc(cc3F)C(=O)c4cn(c5c4c(ccc5)C#C)C(=O)N(C)C
PubChem154087
Formal Charge0
Total Atoms58
Total Chiral Atoms0
Total Bonds62
Total Aromatic Bonds26

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP25105
Sequence
>5ZKQ_Chain_R
SHMDSEFRY TLFPIVYSI IFVLGVIAN GYVLWVFAR LYPFNEIKI 
FMVNLTMAD MLFLITLPL WIVYYQNQG NWILPKFLC NVAGCLFFI 
NTYCSVAFL GVITYNRYQ AVTRPIQAN TRKRGISLS LVIWVAIVG 
AASYFLILD STNTVPDSA GSGDVTRCF EHYEKGSVP VLIIHIFIV 
FSFFLVFLI ILFCNLVII RTLLMQPVA EVKRRDLWM ACTVLAVFI 
ICFVPHHVV QLPWTLAEL GFQDSKFHQ AINDAHQVT LCLLSTNCV 
LNPVIYCFL TKKF


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 network is also present in following consensuses:
IdComponents
paf_off5ZKQ-PAF-ABT-491
5ZKP-PAF-Foropafant (SR27417)

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
5ZKPALipidPlatelet-activating factorPAFHomo sapiensForopafant (SR27417)--2.812018-06-2010.1038/s41594-018-0068-y
5ZKQALipidPlatelet-activating factorPAFHomo sapiensABT-491--2.92018-06-2010.1038/s41594-018-0068-y




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 5ZKQ.zip



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