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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
4ork GDP Bifunctional AAC/APH 2.3.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ork GDPBifunctional AAC/APH 2.3.1 0.991
5iqb GNPBifunctional AAC/APH 2.3.1 0.837
5iqf GDPBifunctional AAC/APH 2.3.1 0.804
5iqi GNPBifunctional AAC/APH 2.3.1 0.802
5iqa GNPBifunctional AAC/APH 2.3.1 0.801
5byl GCPBifunctional AAC/APH 2.3.1 0.797
5iqh GNPBifunctional AAC/APH 2.3.1 0.795
5iqe GNPBifunctional AAC/APH 2.3.1 0.792
5iqd GNPBifunctional AAC/APH 2.3.1 0.791
5iqg GDPBifunctional AAC/APH 2.3.1 0.786
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.763
4ceg ADPAurora kinase A 2.7.11.1 0.761
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.760
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.759
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.758
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.752
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.751
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.750
2pyw ADPMethylthioribose kinase 2.7.1.100 0.749
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.748
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.747
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.743
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.743
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.742
4dee ADPAurora kinase A 2.7.11.1 0.740
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.739
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
3c4z ADPRhodopsin kinase / 0.737
5ce3 ADPProtein kinase YopO / 0.737
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.733
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.729
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.729
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.729
1mq4 ADPAurora kinase A 2.7.11.1 0.728
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.728
2pui ADPMethylthioribose kinase 2.7.1.100 0.728
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.728
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.727
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.726
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.722
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.721
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.721
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.720
2pup ADPMethylthioribose kinase 2.7.1.100 0.718
3tdv GDPGentamicin resistance protein / 0.718
4utd ACPAurora kinase A 2.7.11.1 0.718
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.717
3tdw GDPGentamicin resistance protein / 0.715
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.715
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.713
3c50 ADPRhodopsin kinase / 0.712
4o4d ATPKinase / 0.711
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.710
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.708
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.708
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.705
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.703
2pul ACPMethylthioribose kinase 2.7.1.100 0.702
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.702
4gyi ADPUncharacterized protein / 0.702
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.698
3qc9 ADPRhodopsin kinase / 0.697
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.697
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.696
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.695
5dn3 ATPAurora kinase A 2.7.11.1 0.694
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.693
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.692
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.692
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.690
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.690
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.689
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.687
2pun ACPMethylthioribose kinase 2.7.1.100 0.686
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.685
2olc ADPMethylthioribose kinase 2.7.1.100 0.685
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.684
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.683
4n57 ADPAPH(2'')-Id / 0.683
5dos ATPAurora kinase A 2.7.11.1 0.683
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.682
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.682
3wnz ADPAlanine--anticapsin ligase / 0.681
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.680
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.679
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
5dt4 ATPAurora kinase A 2.7.11.1 0.679
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.678
3g6w GTPUracil phosphoribosyltransferase 2.4.2.9 0.678
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.678
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.677
4bn1 ADPAurora kinase A 2.7.11.1 0.676
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.676
5dt3 ATPAurora kinase A 2.7.11.1 0.676
5dr2 ATPAurora kinase A 2.7.11.1 0.675
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.674
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.674
2hgs ADPGlutathione synthetase 6.3.2.3 0.673
3ori AGSSerine/threonine protein kinase / 0.673
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.672
5drd ATPAurora kinase A 2.7.11.1 0.672
3bu5 ATPInsulin receptor 2.7.10.1 0.671
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.670
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.669
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.669
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.668
2dwb ANPAurora kinase A 2.7.11.1 0.668
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.668
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.668
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.666
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
3t8o ATPRhodopsin kinase / 0.665
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
2zdg ADPD-alanine--D-alanine ligase / 0.662
5dnr ATPAurora kinase A 2.7.11.1 0.662
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.661
4fhp UTPTerminal uridylyltransferase cid1 / 0.661
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.660
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.660
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.658
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.653
4dtb GMPAPH(2'')-Id / 0.653
3c4w ATPRhodopsin kinase / 0.652
4ysj ADPCalmodulin-like domain protein kinase / 0.652
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
1r89 CTPCCA-adding enzyme 2.7.7.72 0.651
2pz5 ACPFibroblast growth factor receptor 2 / 0.651
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.651
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.651
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.650
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.650
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.650
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.650