Structural Bioinformatics Group
Division of Molecular Biosciences
Faculty of Natural Sciences


3DLigandSite -Ligand binding site prediction Server

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3DLigandSite Results

Submission Successful - Job-id: example4    Current Status: STATUS:finished


All Jobs are run on a queue system. You will receive an email confirming submission and one once 3dLigandSite has run. Jobs generally take between 1-3 hours to complete depending on complexity and server load.
you can also view your job's progress and results on this page It will refresh every 30 second until the job is completed
You can bookmark this page: http://www.sbg.bio.imperial.ac.uk/3dligandsite/3dligand_report_p2.cgi?jobid=example4

Please cite: Wass M.N., Kelley L.A. and Sternberg M.J. (2010) 3DLigandSite: predicting ligand-binding sites using similar structures.NAR 38, W469-73. PubMed

The structural library currently used by 3DLigandSite is based on the PDB as of 20 January 2010

Submission Details
Email: mw3@ic.ac.uk
Unique Job identifier: example4
Description: T0483 example
Date: Sun Feb 7 12:07:06 GMT 2010
Submission Type: structure
Query Seq: GLAACEGEYSQKYSTMSPLGSGAFGFVWTAVDKEKNKEVVVKFIKKEKVLEDCWIEDPKL
GKVTLEIAILSRVEHANIIKVLDIFENQGFFQLVMEKHSGLDLFAFIDRHPRLDEPLASY
IFRQLVSAVGYLRLKDIIHRDIKDENIVIAEDFTIKLIDFGSAAYLERGKLFYTFCGTIE
YCAPEVLMGNPYRGPELEMWSLGVTLYTLVFEENPFCELEETVEAAIHPPYLVSKELMSL
VSGLLQPVPERRTTLEKLVTDPWVTQPVNLADYTWEEVFRVNKPESGVLSAASLEMGNRS
LSDVAQAQELCGGE

Structural Model
User provided file: T0483example.pdb
Structural Search
confidence data from search of structural library with Mammoth
Average lnE:26.6587
Maximum LnE:28.43
Min LnE:26.22

Ligand Clusters Identified
Note prediction based on first cluster
Click on other clusters to view the potential sites associated with them
MAMMOTH Scores
ClusterLigandsStructuresAvminmax
1332326.726.228.4
22226.426.326.5
31126.226.226.2
41126.526.526.5
51126.926.926.9

Predicted Binding Site
ResidueAmino
acid
contactav distanceJS
divergence
59LYS140.000.75
61LYS130.370.38
92ILE140.000.54
108MET90.600.60
109GLU140.000.82
110LYS140.000.65
111HIS140.000.53
113SER120.400.48
116ASP140.230.76
159GLU300.100.83
160ASN90.660.87
162VAL100.490.65
172ILE190.120.49
173ASP270.160.85
181GLU230.200.24
182ARG280.170.21
183GLY90.000.35
Heterogens present in Predicted Binding Site
HeterogenCountsource structures
STU 43d7t_B,1snu_B,1sm2_B,3d7t_A
ADP 41ol7_A,1mq4_A,3dls_F,1ol5_A
MG 192w5b_A,1ol7_A,1mq4_A,1x8b_A,2v7a_B,
2vwy_A,3dls_F,2vwz_A,2gs7_A,2g1t_B,
3is5_A,1ol5_A,2r5t_A
AMP 11yxu_C
ATP 52biy_A,1h1w_A,1ql6_A,1ol6_A,1phk_A

Structural View of Prediction

Download model and pymol Script (gzip)
Download model
Download pymol Script

Display Modification

Whole protein

Predicted residues

Heterogens


View

Prediction colour legend:Other residuesPredicted Binding Site
Conservation Score Colour legend: 0-0.15 0.16-0.30 0.31-0.40 0.41-0.50
0.51-0.60 0.61-0.70 0.71-0.80 0.81-1.00

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© Structural Bioinformatics Group, Imperial College, London
Mark Wass