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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
4ysj ADP Calmodulin-like domain protein kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ysj ADPCalmodulin-like domain protein kinase / 1.025
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.881
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.839
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.828
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.828
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.827
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.827
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.821
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.820
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.816
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.815
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.810
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.809
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.808
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.801
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.800
5dt3 ATPAurora kinase A 2.7.11.1 0.792
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.791
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.789
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.789
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.789
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.784
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.784
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.782
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.780
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.780
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.779
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.778
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.776
4utd ACPAurora kinase A 2.7.11.1 0.776
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.775
3gub GUBDeath-associated protein kinase 1 2.7.11.1 0.774
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.774
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.773
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.773
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.770
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.768
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.768
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.765
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.765
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.764
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.764
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.763
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.761
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.759
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.758
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.758
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.758
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.757
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.757
4dee ADPAurora kinase A 2.7.11.1 0.756
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.756
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.756
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.753
5dn3 ATPAurora kinase A 2.7.11.1 0.752
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.750
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.749
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.748
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.747
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.744
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.743
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.743
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.743
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.741
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.738
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.730
2pui ADPMethylthioribose kinase 2.7.1.100 0.729
1mq4 ADPAurora kinase A 2.7.11.1 0.728
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.728
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.727
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.727
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.725
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.725
5dt4 ATPAurora kinase A 2.7.11.1 0.724
3agl A03cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.723
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.723
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.721
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.719
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.717
4bn1 ADPAurora kinase A 2.7.11.1 0.717
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.716
3gu8 3GUDeath-associated protein kinase 1 2.7.11.1 0.716
5dr2 ATPAurora kinase A 2.7.11.1 0.716
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.715
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.714
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.714
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.712
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.711
3qc9 ADPRhodopsin kinase / 0.711
3wnz ADPAlanine--anticapsin ligase / 0.711
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.709
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.709
4qny ANPMitogen activated protein kinase, putative / 0.709
5ce3 ADPProtein kinase YopO / 0.709
2olc ADPMethylthioribose kinase 2.7.1.100 0.708
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.707
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.707
3nie ANPMitogen-activated protein kinase / 0.707
4pds ANPSerine/threonine-protein kinase RAD53 2.7.12.1 0.707
5dnr ATPAurora kinase A 2.7.11.1 0.707
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.706
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.706
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.706
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.705
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.703
5dos ATPAurora kinase A 2.7.11.1 0.703
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.702
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.702
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.702
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.701
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.701
3llt ANPProtein serine/threonine kinase-1 / 0.701
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.701
2dwb ANPAurora kinase A 2.7.11.1 0.700
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.700
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.700
4ix5 ANPUncharacterized protein / 0.699
3c50 ADPRhodopsin kinase / 0.698
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.697
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.697
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.696
4ffr ATPUncharacterized protein / 0.696
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.696
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.696
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.694
1px2 ATPSynapsin-1 / 0.693
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.693
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.692
3hrf ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.692
4gyi ADPUncharacterized protein / 0.692
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.690
5drd ATPAurora kinase A 2.7.11.1 0.690
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.689
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.689
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.688
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.686
3wow ANPCasein kinase II subunit alpha 2.7.11.1 0.686
4c3r ACPAurora kinase A 2.7.11.1 0.686
4xlv ACPInsulin receptor 2.7.10.1 0.686
3c4z ADPRhodopsin kinase / 0.685
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.684
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.684
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.682
4ceg ADPAurora kinase A 2.7.11.1 0.682
3cly ACPFibroblast growth factor receptor 2 / 0.681
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.681
2pul ACPMethylthioribose kinase 2.7.1.100 0.680
3oro AGSSerine/threonine protein kinase / 0.680
5iqh GNPBifunctional AAC/APH 2.3.1 0.680
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.679
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.679
2hgs ADPGlutathione synthetase 6.3.2.3 0.678
3ort AGSSerine/threonine protein kinase / 0.678
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.678
1ol5 ADPAurora kinase A 2.7.11.1 0.677
3bu5 ATPInsulin receptor 2.7.10.1 0.677
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.676
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.676
4ffl ADPUncharacterized protein / 0.676
5iqb GNPBifunctional AAC/APH 2.3.1 0.676
3t8o ATPRhodopsin kinase / 0.675
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.675
5byl GCPBifunctional AAC/APH 2.3.1 0.675
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.674
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.674
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.673
4o0w ADNAurora kinase A 2.7.11.1 0.673
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.672
2wqe ADPAurora kinase A 2.7.11.1 0.671
5eg3 ACPFibroblast growth factor receptor 2 / 0.671
1m0w ANPGlutathione synthetase 6.3.2.3 0.670
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.670
4oac ADPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.670
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.670
5ckw ANPUncharacterized protein / 0.670
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.669
4riy ADPEpidermal growth factor receptor 2.7.10.1 0.669
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.668
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.667
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.666
2zdg ADPD-alanine--D-alanine ligase / 0.666
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.666
4ct2 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.665
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.664
2b56 UTPRNA editing complex protein MP57 / 0.664
3v0m 5GWHisto-blood group ABO system transferase / 0.664
3zo1 SIJcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
4c3p ACPAurora kinase A 2.7.11.1 0.664
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.664
4o0u ADNAurora kinase A 2.7.11.1 0.664
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.663
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.662
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.659
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.658
3rv4 ADPBiotin carboxylase 6.3.4.14 0.658
3t7o UPGGlycogenin-1 2.4.1.186 0.658
5l8j ADPAurora kinase A 2.7.11.1 0.658
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.657
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.657
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.657
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.655
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.655
3nyn SGVG protein-coupled receptor kinase 6 2.7.11.16 0.654
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.654
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.653
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.653
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.653
4n57 ADPAPH(2'')-Id / 0.653
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.652
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.652
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.652
4ork GDPBifunctional AAC/APH 2.3.1 0.652
3tdw GDPGentamicin resistance protein / 0.651
3wo1 ADPAlanine--anticapsin ligase / 0.651