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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
3dnt ATP Serine/threonine-protein kinase toxin HipA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dnt ATPSerine/threonine-protein kinase toxin HipA / 1.260
3tpt ADPSerine/threonine-protein kinase toxin HipA / 1.022
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.862
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.792
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.791
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.789
3c4z ADPRhodopsin kinase / 0.783
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.781
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.774
2pup ADPMethylthioribose kinase 2.7.1.100 0.766
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.755
2pyw ADPMethylthioribose kinase 2.7.1.100 0.752
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.750
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.749
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.742
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.742
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.740
4ceg ADPAurora kinase A 2.7.11.1 0.739
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.738
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.737
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.734
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.733
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.733
1mq4 ADPAurora kinase A 2.7.11.1 0.731
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.731
4n57 ADPAPH(2'')-Id / 0.731
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
4ork GDPBifunctional AAC/APH 2.3.1 0.728
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.727
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.725
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.724
5byl GCPBifunctional AAC/APH 2.3.1 0.724
3bu5 ATPInsulin receptor 2.7.10.1 0.723
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.718
5dos ATPAurora kinase A 2.7.11.1 0.717
4bn1 ADPAurora kinase A 2.7.11.1 0.716
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.715
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.715
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.715
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.714
5dnr ATPAurora kinase A 2.7.11.1 0.714
3ori AGSSerine/threonine protein kinase / 0.712
5iqb GNPBifunctional AAC/APH 2.3.1 0.712
5dt4 ATPAurora kinase A 2.7.11.1 0.711
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.710
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.710
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.709
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.707
1m0w ANPGlutathione synthetase 6.3.2.3 0.707
2fsn ADPArchaeal actin homolog / 0.706
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.706
3wnz ADPAlanine--anticapsin ligase / 0.706
4gyi ADPUncharacterized protein / 0.706
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.705
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.705
5ce3 ADPProtein kinase YopO / 0.705
2dwb ANPAurora kinase A 2.7.11.1 0.701
4o4e ATPKinase / 0.701
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.700
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.700
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.698
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.698
4o4f ATPKinase / 0.697
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.696
4ffr ATPUncharacterized protein / 0.696
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
3hzi ATPSerine/threonine-protein kinase toxin HipA / 0.695
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
5iqh GNPBifunctional AAC/APH 2.3.1 0.695
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.693
3cly ACPFibroblast growth factor receptor 2 / 0.693
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.692
4qny ANPMitogen activated protein kinase, putative / 0.692
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.690
3c4x ATPRhodopsin kinase / 0.690
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.690
4utd ACPAurora kinase A 2.7.11.1 0.690
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.689
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.689
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.689
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.689
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.689
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.686
4ysj ADPCalmodulin-like domain protein kinase / 0.686
5dr2 ATPAurora kinase A 2.7.11.1 0.686
2x0q ATPAlcaligin biosynthesis protein / 0.684
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.683
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.683
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.682
4xlv ACPInsulin receptor 2.7.10.1 0.682
5dn3 ATPAurora kinase A 2.7.11.1 0.682
4c3r ACPAurora kinase A 2.7.11.1 0.681
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.680
2olc ADPMethylthioribose kinase 2.7.1.100 0.680
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.680
3t8o ATPRhodopsin kinase / 0.680
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.680
4jrn ANPRhoptry kinase family protein / 0.678
2pui ADPMethylthioribose kinase 2.7.1.100 0.677
2pul ACPMethylthioribose kinase 2.7.1.100 0.677
4ffm ADPUncharacterized protein / 0.677
1px2 ATPSynapsin-1 / 0.676
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.676
4c3p ACPAurora kinase A 2.7.11.1 0.676
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.675
2hgs ADPGlutathione synthetase 6.3.2.3 0.675
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.675
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.675
5dt3 ATPAurora kinase A 2.7.11.1 0.675
2vp0 TTPDeoxynucleoside kinase / 0.674
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.674
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.674
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.672
4q5h ANPProtein kinase OspG 2.7 0.672
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.671
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.671
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.671
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.670
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.670
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.670
4ffl ADPUncharacterized protein / 0.669
5drd ATPAurora kinase A 2.7.11.1 0.669
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.668
3qc9 ADPRhodopsin kinase / 0.668
1u54 ACPActivated CDC42 kinase 1 / 0.667
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.667
5iqi GNPBifunctional AAC/APH 2.3.1 0.667
1oqm UD2Beta-1,4-galactosyltransferase 1 / 0.666
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.666
4fu0 ADPD-alanine--D-alanine ligase / 0.666
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.665
5iqf GDPBifunctional AAC/APH 2.3.1 0.664
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.663
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.663
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.663
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.663
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.663
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.663
1zc3 GNPRas-related protein Ral-A / 0.662
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.661
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.661
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.661
2pml ANPUncharacterized protein / 0.660
5l8l ADPAurora kinase A 2.7.11.1 0.660
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.659
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.659
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.658
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
2vnh FADNADPH:ferredoxin reductase / 0.657
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.657
5c1o ANPD-alanine--D-alanine ligase / 0.657
1s16 ANPDNA topoisomerase 4 subunit B / 0.656
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.656
3rv4 ADPBiotin carboxylase 6.3.4.14 0.655
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.654
2zgy GDPPlasmid segregation protein ParM / 0.654
3ftq GNPSeptin-2 / 0.654
3g8d ADPBiotin carboxylase 6.3.4.14 0.654
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.654
4ee3 UDHBeta-1,4-galactosyltransferase 1 / 0.654
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.654
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.653
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.653
5iqe GNPBifunctional AAC/APH 2.3.1 0.653
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.652
1yro GDUBeta-1,4-galactosyltransferase 1 / 0.652
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.652
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
4idn GNPAtlastin-1 3.6.5 0.652
4lv5 ADPRhoptry protein 5B / 0.652
1ol5 ADPAurora kinase A 2.7.11.1 0.651
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.650
3tdw GDPGentamicin resistance protein / 0.650
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.650
4o4d ATPKinase / 0.650