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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
4zgn ATP Cell division cycle protein 123

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4zgn ATPCell division cycle protein 123 / 1.241
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.741
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.724
4dee ADPAurora kinase A 2.7.11.1 0.724
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.710
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.710
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.705
1ol5 ADPAurora kinase A 2.7.11.1 0.705
2pul ACPMethylthioribose kinase 2.7.1.100 0.702
2pup ADPMethylthioribose kinase 2.7.1.100 0.699
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.698
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.696
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.695
4ceg ADPAurora kinase A 2.7.11.1 0.692
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.690
5dt3 ATPAurora kinase A 2.7.11.1 0.690
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.689
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.687
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.686
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.685
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.684
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
2j9g ADPBiotin carboxylase 6.3.4.14 0.682
3rv4 ADPBiotin carboxylase 6.3.4.14 0.681
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.681
2olc ADPMethylthioribose kinase 2.7.1.100 0.680
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.680
1pk8 ATPSynapsin-1 / 0.679
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.679
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.678
2pml ANPUncharacterized protein / 0.677
3nie ANPMitogen-activated protein kinase / 0.677
5dnr ATPAurora kinase A 2.7.11.1 0.676
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.675
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.675
4ffr ATPUncharacterized protein / 0.674
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.673
3r5f ATPD-alanine--D-alanine ligase / 0.673
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.671
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.671
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.668
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.667
3tw6 ADPPyruvate carboxylase / 0.666
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
2pui ADPMethylthioribose kinase 2.7.1.100 0.664
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.662
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.662
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.661
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.661
1ol7 ADPAurora kinase A 2.7.11.1 0.660
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.660
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.659
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.659
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.659
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.658
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.657
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.657
5f1c ATPUncharacterized protein / 0.657
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.656
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.656
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.656
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.656
3cly ACPFibroblast growth factor receptor 2 / 0.655
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.653
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.653
1q3g UDAUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.652
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.652
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.651
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.651