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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
4m42 ATP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4m42 ATPDNA-directed DNA polymerase / 1.192
4fj5 DTPDNA-directed DNA polymerase / 1.143
4fjj TTPDNA-directed DNA polymerase / 1.130
4fjh DGTDNA-directed DNA polymerase / 1.123
4dtp DGTDNA-directed DNA polymerase / 1.084
4fjl DGTDNA-directed DNA polymerase / 1.076
3ne6 DCPDNA-directed DNA polymerase / 1.074
4fk4 DGTDNA-directed DNA polymerase / 1.072
4m3x ATPDNA-directed DNA polymerase / 1.070
4dtx TTPDNA-directed DNA polymerase / 1.049
3sup DCPDNA-directed DNA polymerase / 1.046
4fjm DCPDNA-directed DNA polymerase / 1.035
4khy TTPDNA-directed DNA polymerase / 1.025
3lzj CTPDNA-directed DNA polymerase / 1.024
4dtj TTPDNA-directed DNA polymerase / 1.018
4m3t ATPDNA-directed DNA polymerase / 1.010
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.962
4dto DCPDNA-directed DNA polymerase / 0.908
3g6x DGTDNA polymerase iota 2.7.7.7 0.881
4dtm DCPDNA-directed DNA polymerase / 0.851
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.821
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.805
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.794
3q23 G2PVirion DNA-directed RNA polymerase / 0.788
3au2 DGTDNA polymerase beta family (X family) / 0.778
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.769
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.767
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.753
2q66 ATPPoly(A) polymerase 2.7.7.19 0.749
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.712
1r89 CTPCCA-adding enzyme 2.7.7.72 0.711
4u03 GTPCyclic GMP-AMP synthase / 0.704
4k97 ATPCyclic GMP-AMP synthase / 0.700
1r8b ATPCCA-adding enzyme 2.7.7.72 0.698
1r8c UTPCCA-adding enzyme 2.7.7.72 0.696
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.695
4xj3 GTPCyclic GMP-AMP synthase / 0.691
5a2w AGSMitochondrial poly(A) polymerase / 0.689
4xj4 3ATCyclic GMP-AMP synthase / 0.683
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.681
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.674
3hiy UTPUncharacterized protein / 0.671
2o4g TMPThree-prime repair exonuclease 1 3.1.11.2 0.670
4kgm ATPUncharacterized protein / 0.665
2jlr ANPGenome polyprotein 3.4.21.91 0.659
1cjv DADAdenylate cyclase type 2 / 0.658
1cjv DADAdenylate cyclase type 5 / 0.658
1fcb FMNCytochrome b2, mitochondrial 1.1.2.3 0.658
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 0.658
3m0e ATPTranscriptional regulator (NtrC family) / 0.657
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
3dds 26BGlycogen phosphorylase, liver form 2.4.1.1 0.652
3ftq GNPSeptin-2 / 0.652
5i4n ATPTyrosine-protein kinase JAK2 / 0.652
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
3g8c ADPBiotin carboxylase 6.3.4.14 0.650