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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
3tdw GDP Gentamicin resistance protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3tdw GDPGentamicin resistance protein / 1.071
3tdv GDPGentamicin resistance protein / 1.014
5iqf GDPBifunctional AAC/APH 2.3.1 0.898
5iqb GNPBifunctional AAC/APH 2.3.1 0.820
5iqe GNPBifunctional AAC/APH 2.3.1 0.820
5iqa GNPBifunctional AAC/APH 2.3.1 0.816
5iqd GNPBifunctional AAC/APH 2.3.1 0.797
5iqi GNPBifunctional AAC/APH 2.3.1 0.796
5byl GCPBifunctional AAC/APH 2.3.1 0.786
5iqh GNPBifunctional AAC/APH 2.3.1 0.754
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.739
5iqg GDPBifunctional AAC/APH 2.3.1 0.734
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.729
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.727
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.722
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.719
4ceg ADPAurora kinase A 2.7.11.1 0.719
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.718
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.717
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.715
4ork GDPBifunctional AAC/APH 2.3.1 0.715
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.715
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.713
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.711
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.711
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.711
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.710
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.709
1mq4 ADPAurora kinase A 2.7.11.1 0.706
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.705
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.703
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.702
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.702
4n57 ADPAPH(2'')-Id / 0.702
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.698
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.694
2pup ADPMethylthioribose kinase 2.7.1.100 0.692
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.688
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.686
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.686
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.685
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.682
5dn3 ATPAurora kinase A 2.7.11.1 0.682
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.680
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.679
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.677
4dee ADPAurora kinase A 2.7.11.1 0.677
5drd ATPAurora kinase A 2.7.11.1 0.676
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.675
2pui ADPMethylthioribose kinase 2.7.1.100 0.674
3c4z ADPRhodopsin kinase / 0.674
5dos ATPAurora kinase A 2.7.11.1 0.674
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.673
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.673
3qc9 ADPRhodopsin kinase / 0.672
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.672
4utd ACPAurora kinase A 2.7.11.1 0.672
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.671
4dtb GMPAPH(2'')-Id / 0.671
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.668
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.666
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.665
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.664
5dr2 ATPAurora kinase A 2.7.11.1 0.664
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.662
3c50 ADPRhodopsin kinase / 0.662
3ori AGSSerine/threonine protein kinase / 0.662
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.662
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.661
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.661
3bu5 ATPInsulin receptor 2.7.10.1 0.660
3cly ACPFibroblast growth factor receptor 2 / 0.660
4ffr ATPUncharacterized protein / 0.660
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.659
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.659
5dnr ATPAurora kinase A 2.7.11.1 0.659
5dt4 ATPAurora kinase A 2.7.11.1 0.659
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.658
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.658
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.658
3oro AGSSerine/threonine protein kinase / 0.657
5dt3 ATPAurora kinase A 2.7.11.1 0.657
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.656
2pyw ADPMethylthioribose kinase 2.7.1.100 0.656
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.656
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.656
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.655
3pff ADPATP-citrate synthase 2.3.3.8 0.655
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.654
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.653
2olc ADPMethylthioribose kinase 2.7.1.100 0.653
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.653
2pul ACPMethylthioribose kinase 2.7.1.100 0.652
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.652
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.651
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4ffl ADPUncharacterized protein / 0.651
4ysj ADPCalmodulin-like domain protein kinase / 0.651
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.650
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.650