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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3gcm 5GP Polyribonucleotide nucleotidyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3gcm 5GPPolyribonucleotide nucleotidyltransferase / 0.784
1n38 U3HRNA-directed RNA polymerase lambda-3 2.7.7.48 0.744
1nmd ATPMajor actin / 0.744
1xxj UNCUricase 1.7.3.3 0.744
2cgw 3C3Serine/threonine-protein kinase Chk1 2.7.11.1 0.744
2oap ANPType II secretion system protein (GspE-2) / 0.744
2z7q ACPRibosomal protein S6 kinase alpha-1 2.7.11.1 0.744
3fzf ATPHeat shock cognate 71 kDa protein / 0.744
3u9d ATPActin, alpha skeletal muscle / 0.744
3ypi PGHTriosephosphate isomerase 5.3.1.1 0.744
3zzn ADPL-lactate dehydrogenase / 0.744
4e5l DBHPolymerase acidic protein / 0.744
4y8v ADPAcyl-CoA synthetase (NDP forming) / 0.744
4dsj DGTDNA polymerase I / 0.675
4dpg APCLysine--tRNA ligase 6.1.1.6 0.672
5ayj MUAUric acid degradation bifunctional protein 1.7.3.3 0.671
2puc GUNHTH-type transcriptional repressor PurR / 0.667
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.660
1h48 C5P2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 4.6.1.12 0.660
2hru ADPPhosphoribosylformylglycinamidine synthase subunit PurL / 0.660
2hs4 ACPPhosphoribosylformylglycinamidine synthase subunit PurL / 0.660
2xtn GTPGTPase IMAP family member 2 / 0.660
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.660
4cdg ADPBloom syndrome protein 3.6.4.12 0.660
4o3m ADPBloom syndrome protein 3.6.4.12 0.660
4br7 AU1Ectonucleoside triphosphate diphosphohydrolase I / 0.656
2iuu ADPDNA translocase FtsK / 0.651
4hrq AZGCytidine and deoxycytidylate deaminase zinc-binding region / 0.651
2zfi ADPKinesin-like protein KIF1A / 0.650