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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
3c50 ADP Rhodopsin kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3c50 ADPRhodopsin kinase / 0.922
3c4z ADPRhodopsin kinase / 0.905
4dee ADPAurora kinase A 2.7.11.1 0.877
3qc9 ADPRhodopsin kinase / 0.862
3t8o ATPRhodopsin kinase / 0.831
4ceg ADPAurora kinase A 2.7.11.1 0.827
1mq4 ADPAurora kinase A 2.7.11.1 0.824
3c4w ATPRhodopsin kinase / 0.815
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.807
2pui ADPMethylthioribose kinase 2.7.1.100 0.797
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.796
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.790
5dos ATPAurora kinase A 2.7.11.1 0.790
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.788
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.788
5dt3 ATPAurora kinase A 2.7.11.1 0.788
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.787
5dn3 ATPAurora kinase A 2.7.11.1 0.785
2pun ACPMethylthioribose kinase 2.7.1.100 0.784
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.779
3c4x ATPRhodopsin kinase / 0.779
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.777
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.775
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.774
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.773
4utd ACPAurora kinase A 2.7.11.1 0.773
2pul ACPMethylthioribose kinase 2.7.1.100 0.772
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.770
3cly ACPFibroblast growth factor receptor 2 / 0.770
2pup ADPMethylthioribose kinase 2.7.1.100 0.769
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.765
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.763
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.760
5dnr ATPAurora kinase A 2.7.11.1 0.760
2olc ADPMethylthioribose kinase 2.7.1.100 0.758
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.758
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.758
2pyw ADPMethylthioribose kinase 2.7.1.100 0.757
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.754
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.753
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.753
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.753
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.750
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.748
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.747
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.742
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.742
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.740
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.740
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.739
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.739
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
5dt4 ATPAurora kinase A 2.7.11.1 0.739
4bn1 ADPAurora kinase A 2.7.11.1 0.738
5drd ATPAurora kinase A 2.7.11.1 0.738
5dr2 ATPAurora kinase A 2.7.11.1 0.736
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.735
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.735
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.733
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.731
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.731
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.731
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.729
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
3ori AGSSerine/threonine protein kinase / 0.726
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.723
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.720
3orm AGSSerine/threonine protein kinase / 0.718
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.716
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.716
5byl GCPBifunctional AAC/APH 2.3.1 0.716
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.714
4q5h ANPProtein kinase OspG 2.7 0.714
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.712
4ork GDPBifunctional AAC/APH 2.3.1 0.712
4xlv ACPInsulin receptor 2.7.10.1 0.711
3bu5 ATPInsulin receptor 2.7.10.1 0.710
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.709
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
1ol6 ATPAurora kinase A 2.7.11.1 0.708
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.708
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.708
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.708
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.708
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.707
5iqh GNPBifunctional AAC/APH 2.3.1 0.706
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.705
4ix5 ANPUncharacterized protein / 0.705
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.702
2dwb ANPAurora kinase A 2.7.11.1 0.700
5iqb GNPBifunctional AAC/APH 2.3.1 0.700
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.698
4ysj ADPCalmodulin-like domain protein kinase / 0.698
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.696
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.696
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.696
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.694
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.694
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.694
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.694
3llt ANPProtein serine/threonine kinase-1 / 0.693
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.693
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.693
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.692
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.692
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.691
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.691
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.690
3nie ANPMitogen-activated protein kinase / 0.690
3q5i ANPProtein kinase, putative / 0.690
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.688
1m0w ANPGlutathione synthetase 6.3.2.3 0.687
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.687
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.687
5iqe GNPBifunctional AAC/APH 2.3.1 0.687
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.686
2py3 ACPFibroblast growth factor receptor 2 / 0.686
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.686
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.685
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.685
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.684
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.682
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
4qny ANPMitogen activated protein kinase, putative / 0.682
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.681
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.681
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.681
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.680
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.680
4o4e ATPKinase / 0.679
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
5iqf GDPBifunctional AAC/APH 2.3.1 0.678
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.677
2pz5 ACPFibroblast growth factor receptor 2 / 0.676
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.676
1cm8 ANPMitogen-activated protein kinase 12 / 0.675
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.675
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
5iqa GNPBifunctional AAC/APH 2.3.1 0.675
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.674
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.674
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.674
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.673
4lv8 ADPRhoptry protein 5 C / 0.672
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.671
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
5l8j ADPAurora kinase A 2.7.11.1 0.668
3rv4 ADPBiotin carboxylase 6.3.4.14 0.667
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.666
4wh3 ATPN-acetylhexosamine 1-kinase 2.7.1.162 0.666
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.665
4gyi ADPUncharacterized protein / 0.665
5iqi GNPBifunctional AAC/APH 2.3.1 0.665
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.664
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.663
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.663
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.662
3tdw GDPGentamicin resistance protein / 0.662
4c3r ACPAurora kinase A 2.7.11.1 0.662
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.662
5ce3 ADPProtein kinase YopO / 0.662
1ol7 ADPAurora kinase A 2.7.11.1 0.661
2pzp ACPFibroblast growth factor receptor 2 / 0.660
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
5l8k ADPAurora kinase A 2.7.11.1 0.660
4jrn ANPRhoptry kinase family protein / 0.659
2wqe ADPAurora kinase A 2.7.11.1 0.658
3q60 ATPRhoptry protein 5B / 0.658
5iqd GNPBifunctional AAC/APH 2.3.1 0.658
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
4n57 ADPAPH(2'')-Id / 0.657
1pjk ANPCasein kinase II subunit alpha 2.7.11.1 0.656
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.656
3zfd ANPChromosome-associated kinesin KIF4 / 0.656
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.656
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.655
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.655
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.654
2itv ANPEpidermal growth factor receptor 2.7.10.1 0.654
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.653
3tso GNPRas-related protein Rab-25 / 0.653
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.653
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.653
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.653
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.653
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.652
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.652
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
3vjo ANPEpidermal growth factor receptor 2.7.10.1 0.652
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.652
4f1m ACPProbable serine/threonine-protein kinase roco4 2.7.11.1 0.652
2gs7 ANPEpidermal growth factor receptor 2.7.10.1 0.650
3orl AGSSerine/threonine protein kinase / 0.650
5eg3 ACPFibroblast growth factor receptor 2 / 0.650