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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
3c4w ATP Rhodopsin kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3c4w ATPRhodopsin kinase / 0.921
3t8o ATPRhodopsin kinase / 0.832
3c50 ADPRhodopsin kinase / 0.815
3c4x ATPRhodopsin kinase / 0.800
4ceg ADPAurora kinase A 2.7.11.1 0.800
2dwb ANPAurora kinase A 2.7.11.1 0.791
2pun ACPMethylthioribose kinase 2.7.1.100 0.789
1mq4 ADPAurora kinase A 2.7.11.1 0.787
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.781
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.770
2pyw ADPMethylthioribose kinase 2.7.1.100 0.767
3c4z ADPRhodopsin kinase / 0.762
2pul ACPMethylthioribose kinase 2.7.1.100 0.748
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.748
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.746
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.745
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.742
3nie ANPMitogen-activated protein kinase / 0.741
2pui ADPMethylthioribose kinase 2.7.1.100 0.738
3llt ANPProtein serine/threonine kinase-1 / 0.734
3qc9 ADPRhodopsin kinase / 0.734
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.733
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.732
4dee ADPAurora kinase A 2.7.11.1 0.732
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.728
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.727
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.726
5dt4 ATPAurora kinase A 2.7.11.1 0.724
5l8j ADPAurora kinase A 2.7.11.1 0.724
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.722
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.722
2olc ADPMethylthioribose kinase 2.7.1.100 0.720
2pup ADPMethylthioribose kinase 2.7.1.100 0.720
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.719
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.718
4c3r ACPAurora kinase A 2.7.11.1 0.716
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.715
5dr2 ATPAurora kinase A 2.7.11.1 0.714
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.713
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.712
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.711
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.710
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.710
3cly ACPFibroblast growth factor receptor 2 / 0.710
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.708
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
5dt3 ATPAurora kinase A 2.7.11.1 0.707
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.706
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.703
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.702
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.702
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
5dnr ATPAurora kinase A 2.7.11.1 0.700
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.699
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.699
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.698
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.698
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.698
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.697
5l8k ADPAurora kinase A 2.7.11.1 0.697
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.696
4qny ANPMitogen activated protein kinase, putative / 0.696
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.695
5dos ATPAurora kinase A 2.7.11.1 0.695
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.694
4c3p ACPAurora kinase A 2.7.11.1 0.693
4jrn ANPRhoptry kinase family protein / 0.693
2py3 ACPFibroblast growth factor receptor 2 / 0.692
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.691
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.691
5dn3 ATPAurora kinase A 2.7.11.1 0.690
3q5i ANPProtein kinase, putative / 0.689
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.689
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.688
3oro AGSSerine/threonine protein kinase / 0.688
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.687
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.687
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.686
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
4xlv ACPInsulin receptor 2.7.10.1 0.684
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.683
3bu5 ATPInsulin receptor 2.7.10.1 0.683
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.683
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.682
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.681
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.681
2pzp ACPFibroblast growth factor receptor 2 / 0.680
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.680
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.680
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.679
5drd ATPAurora kinase A 2.7.11.1 0.678
5l8l ADPAurora kinase A 2.7.11.1 0.678
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.677
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
3lct ADPALK tyrosine kinase receptor 2.7.10.1 0.674
3mfu ANPPeripheral plasma membrane protein CASK 2.7.11.1 0.674
4o4d ATPKinase / 0.674
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.672
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.672
3cok ANPSerine/threonine-protein kinase PLK4 2.7.11.21 0.672
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.672
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.671
4bn1 ADPAurora kinase A 2.7.11.1 0.671
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.670
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.670
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.670
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.670
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.669
2pz5 ACPFibroblast growth factor receptor 2 / 0.668
2yeg XQGHeat shock protein HSP 90-alpha / 0.668
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.668
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.668
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.667
3orm AGSSerine/threonine protein kinase / 0.667
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.666
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.666
4lv8 ADPRhoptry protein 5 C / 0.666
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.665
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.665
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.664
3a8w ATPProtein kinase C iota type 2.7.11.13 0.663
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.663
4utd ACPAurora kinase A 2.7.11.1 0.663
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.662
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.662
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.662
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4q5j ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.662
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.659
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.659
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.659
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.658
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.658
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.658
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.658
5iqb GNPBifunctional AAC/APH 2.3.1 0.658
1ol7 ADPAurora kinase A 2.7.11.1 0.657
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.657
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.656
5byl GCPBifunctional AAC/APH 2.3.1 0.656
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.655
1ol5 ADPAurora kinase A 2.7.11.1 0.655
4o0u ADNAurora kinase A 2.7.11.1 0.655
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.655
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.654
3ori AGSSerine/threonine protein kinase / 0.654
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.654
4o1p ANPRibonuclease L / 0.654
3r5f ATPD-alanine--D-alanine ligase / 0.653
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.653
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.652
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.652
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.652
4ork GDPBifunctional AAC/APH 2.3.1 0.652
4xhg ADPUncharacterized protein / 0.652
5ce3 ADPProtein kinase YopO / 0.652
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.651
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.651
4o4f ATPKinase / 0.650
5iqh GNPBifunctional AAC/APH 2.3.1 0.650