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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
4dtp DGT DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dtp DGTDNA-directed DNA polymerase / 1.141
3ne6 DCPDNA-directed DNA polymerase / 1.132
3sup DCPDNA-directed DNA polymerase / 1.101
4fj5 DTPDNA-directed DNA polymerase / 1.094
4m42 ATPDNA-directed DNA polymerase / 1.084
4dtj TTPDNA-directed DNA polymerase / 1.078
4fjh DGTDNA-directed DNA polymerase / 1.078
3lzj CTPDNA-directed DNA polymerase / 1.060
4fjj TTPDNA-directed DNA polymerase / 1.058
4fjl DGTDNA-directed DNA polymerase / 1.058
4dtx TTPDNA-directed DNA polymerase / 1.044
4fk4 DGTDNA-directed DNA polymerase / 1.038
4fjm DCPDNA-directed DNA polymerase / 1.026
4khy TTPDNA-directed DNA polymerase / 1.022
4m3x ATPDNA-directed DNA polymerase / 0.998
4m3t ATPDNA-directed DNA polymerase / 0.997
4dto DCPDNA-directed DNA polymerase / 0.955
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.922
4dtm DCPDNA-directed DNA polymerase / 0.881
3g6x DGTDNA polymerase iota 2.7.7.7 0.872
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.864
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.846
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.770
3au2 DGTDNA polymerase beta family (X family) / 0.765
3q23 G2PVirion DNA-directed RNA polymerase / 0.763
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.754
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.747
4xj4 3ATCyclic GMP-AMP synthase / 0.741
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.740
1cjv DADAdenylate cyclase type 2 / 0.738
1cjv DADAdenylate cyclase type 5 / 0.738
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.723
4k97 ATPCyclic GMP-AMP synthase / 0.715
1r89 CTPCCA-adding enzyme 2.7.7.72 0.712
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.708
5a2w AGSMitochondrial poly(A) polymerase / 0.704
4u03 GTPCyclic GMP-AMP synthase / 0.703
1r8b ATPCCA-adding enzyme 2.7.7.72 0.700
4xj3 GTPCyclic GMP-AMP synthase / 0.700
1r8c UTPCCA-adding enzyme 2.7.7.72 0.698
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.695
2q66 ATPPoly(A) polymerase 2.7.7.19 0.692
4kgk GTPUncharacterized protein / 0.687
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.685
4kgm ATPUncharacterized protein / 0.678
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.677
1e4g ATPCell division protein FtsA / 0.666
2jlr ANPGenome polyprotein 3.4.21.91 0.665
2q0d ATPPoly(A) polymerase, putative / 0.661
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.661
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.656
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3m0e ATPTranscriptional regulator (NtrC family) / 0.656
4m69 ANPReceptor-interacting serine/threonine-protein kinase 3 2.7.11.1 0.653
3g8c ADPBiotin carboxylase 6.3.4.14 0.652
4fvq ATPTyrosine-protein kinase JAK2 / 0.650
4fvr ATPTyrosine-protein kinase JAK2 / 0.650