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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
3lzj CTP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lzj CTPDNA-directed DNA polymerase / 1.109
3ne6 DCPDNA-directed DNA polymerase / 1.088
4dtj TTPDNA-directed DNA polymerase / 1.078
4fjm DCPDNA-directed DNA polymerase / 1.075
4fjj TTPDNA-directed DNA polymerase / 1.073
3sup DCPDNA-directed DNA polymerase / 1.066
4dtp DGTDNA-directed DNA polymerase / 1.060
4dtx TTPDNA-directed DNA polymerase / 1.060
4fjh DGTDNA-directed DNA polymerase / 1.058
4fj5 DTPDNA-directed DNA polymerase / 1.056
4m3t ATPDNA-directed DNA polymerase / 1.042
4fk4 DGTDNA-directed DNA polymerase / 1.041
4fjl DGTDNA-directed DNA polymerase / 1.025
4m42 ATPDNA-directed DNA polymerase / 1.024
4m3x ATPDNA-directed DNA polymerase / 1.014
4khy TTPDNA-directed DNA polymerase / 0.943
4dto DCPDNA-directed DNA polymerase / 0.942
4dtm DCPDNA-directed DNA polymerase / 0.873
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.871
3g6x DGTDNA polymerase iota 2.7.7.7 0.861
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.807
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.786
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.763
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.763
3au2 DGTDNA polymerase beta family (X family) / 0.755
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.739
3q23 G2PVirion DNA-directed RNA polymerase / 0.737
4xj4 3ATCyclic GMP-AMP synthase / 0.725
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.720
2q66 ATPPoly(A) polymerase 2.7.7.19 0.718
1r89 CTPCCA-adding enzyme 2.7.7.72 0.714
1r8b ATPCCA-adding enzyme 2.7.7.72 0.702
4u03 GTPCyclic GMP-AMP synthase / 0.701
1r8c UTPCCA-adding enzyme 2.7.7.72 0.698
2b56 UTPRNA editing complex protein MP57 / 0.682
3ftq GNPSeptin-2 / 0.679
4kgk GTPUncharacterized protein / 0.674
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.671
2jlr ANPGenome polyprotein 3.4.21.91 0.666
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.665
1cjv DADAdenylate cyclase type 2 / 0.662
1cjv DADAdenylate cyclase type 5 / 0.662
3fbc TYDNucleoside diphosphate kinase 2.7.4.6 0.656
5a2w AGSMitochondrial poly(A) polymerase / 0.654
4qm6 GTPMetallophosphoesterase / 0.653
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.651
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3rv4 ADPBiotin carboxylase 6.3.4.14 0.650