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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
4fjm DCP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fjm DCPDNA-directed DNA polymerase / 1.162
4fjj TTPDNA-directed DNA polymerase / 1.136
4fj5 DTPDNA-directed DNA polymerase / 1.113
4fjh DGTDNA-directed DNA polymerase / 1.110
4fjl DGTDNA-directed DNA polymerase / 1.084
4fk4 DGTDNA-directed DNA polymerase / 1.078
3lzj CTPDNA-directed DNA polymerase / 1.075
4m3x ATPDNA-directed DNA polymerase / 1.066
4dtx TTPDNA-directed DNA polymerase / 1.062
4dtj TTPDNA-directed DNA polymerase / 1.055
3ne6 DCPDNA-directed DNA polymerase / 1.048
4m3t ATPDNA-directed DNA polymerase / 1.048
4m42 ATPDNA-directed DNA polymerase / 1.035
3sup DCPDNA-directed DNA polymerase / 1.027
4dtp DGTDNA-directed DNA polymerase / 1.026
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.956
4khy TTPDNA-directed DNA polymerase / 0.953
3g6x DGTDNA polymerase iota 2.7.7.7 0.905
4dto DCPDNA-directed DNA polymerase / 0.905
4dtm DCPDNA-directed DNA polymerase / 0.854
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.771
3q23 G2PVirion DNA-directed RNA polymerase / 0.758
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.748
3au2 DGTDNA polymerase beta family (X family) / 0.744
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.737
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.727
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.727
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.714
5a2w AGSMitochondrial poly(A) polymerase / 0.708
2q66 ATPPoly(A) polymerase 2.7.7.19 0.704
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.696
1r89 CTPCCA-adding enzyme 2.7.7.72 0.695
4xj4 3ATCyclic GMP-AMP synthase / 0.693
1r8b ATPCCA-adding enzyme 2.7.7.72 0.688
1r8c UTPCCA-adding enzyme 2.7.7.72 0.686
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.678
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.668
2jlr ANPGenome polyprotein 3.4.21.91 0.668
3ftq GNPSeptin-2 / 0.668
1oe0 TTPDeoxynucleoside kinase / 0.667
4idp GNPAtlastin-1 3.6.5 0.667
4k97 ATPCyclic GMP-AMP synthase / 0.666
2jcs TTPDeoxynucleoside kinase / 0.658
4lt6 3ATPoly(A) polymerase gamma 2.7.7.19 0.656
4qnr ATPPsp operon transcriptional activator / 0.656
3m0e ATPTranscriptional regulator (NtrC family) / 0.655
2bc9 GNPGuanylate-binding protein 1 / 0.653
3fbc TYDNucleoside diphosphate kinase 2.7.4.6 0.653
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.653
1ei1 ANPDNA gyrase subunit B / 0.652
1s16 ANPDNA topoisomerase 4 subunit B / 0.651
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2o4g TMPThree-prime repair exonuclease 1 3.1.11.2 0.650
4u03 GTPCyclic GMP-AMP synthase / 0.650