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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
1zp9 ATP RIO-type serine/threonine-protein kinase Rio1 2.7.11.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.962
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.896
2pui ADPMethylthioribose kinase 2.7.1.100 0.744
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.744
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.738
2olc ADPMethylthioribose kinase 2.7.1.100 0.733
2pup ADPMethylthioribose kinase 2.7.1.100 0.728
4xlv ACPInsulin receptor 2.7.10.1 0.725
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.722
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.721
2pun ACPMethylthioribose kinase 2.7.1.100 0.720
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.719
2pul ACPMethylthioribose kinase 2.7.1.100 0.718
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.717
3c4z ADPRhodopsin kinase / 0.717
3cly ACPFibroblast growth factor receptor 2 / 0.710
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.709
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
3ori AGSSerine/threonine protein kinase / 0.708
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.705
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.704
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.703
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.702
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.701
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.699
4gyi ADPUncharacterized protein / 0.699
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.697
3bu5 ATPInsulin receptor 2.7.10.1 0.696
4fl3 ANPTyrosine-protein kinase SYK 2.7.10.2 0.696
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.694
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
4o4f ATPKinase / 0.693
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.693
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.692
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.690
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.690
3vjo ANPEpidermal growth factor receptor 2.7.10.1 0.687
3a99 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.686
2py3 ACPFibroblast growth factor receptor 2 / 0.685
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.685
4ffr ATPUncharacterized protein / 0.685
3g8d ADPBiotin carboxylase 6.3.4.14 0.684
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.684
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.683
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.683
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.683
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.683
3bwj ARXcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
3rv4 ADPBiotin carboxylase 6.3.4.14 0.681
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.681
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.680
2p0a ANPSynapsin-3 / 0.680
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.680
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.680
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.680
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.679
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.678
2pz5 ACPFibroblast growth factor receptor 2 / 0.678
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.678
3kn5 ANPRibosomal protein S6 kinase alpha-5 2.7.11.1 0.678
3vjn ANPEpidermal growth factor receptor 2.7.10.1 0.678
4o4e ATPKinase / 0.678
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.677
4dee ADPAurora kinase A 2.7.11.1 0.676
5dos ATPAurora kinase A 2.7.11.1 0.676
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.675
4ceg ADPAurora kinase A 2.7.11.1 0.675
2cjm ATPCyclin-dependent kinase 2 2.7.11.22 0.674
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.674
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.674
3fzp AGSProtein-tyrosine kinase 2-beta 2.7.10.2 0.673
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.673
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.673
4b8l A0PAurora kinase B-A 2.7.11.1 0.673
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.673
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.673
4uya AGSMitogen-activated protein kinase kinase kinase 21 2.7.11.25 0.673
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.672
3c4w ATPRhodopsin kinase / 0.672
3tw6 ADPPyruvate carboxylase / 0.672
1zy5 ANPeIF-2-alpha kinase GCN2 / 0.670
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.670
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.670
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.669
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
5eg3 ACPFibroblast growth factor receptor 2 / 0.669
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.668
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.668
4gva ADPMitogen-activated protein kinase 1 2.7.11.24 0.668
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.667
1ol6 ATPAurora kinase A 2.7.11.1 0.667
3agl A03cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.667
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.667
4q5h ANPProtein kinase OspG 2.7 0.667
4ysj ADPCalmodulin-like domain protein kinase / 0.667
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.666
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.666
3juh ANPCasein kinase II subunit alpha 2.7.11.1 0.666
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.666
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.665
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.665
4bn1 ADPAurora kinase A 2.7.11.1 0.665
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.664
2j9g ADPBiotin carboxylase 6.3.4.14 0.664
3a7h ATPSerine/threonine-protein kinase 24 2.7.11.1 0.664
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.664
1u54 ACPActivated CDC42 kinase 1 / 0.663
3c50 ADPRhodopsin kinase / 0.663
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.663
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.663
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.663
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.662
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.662
3lij ANPCalcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands / 0.662
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.662
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.662
4dt8 ADNAPH(2'')-Id / 0.662
4h3p ANPMitogen-activated protein kinase 1 2.7.11.24 0.662
1xkd NAPIsocitrate dehydrogenase [NADP] / 0.661
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.661
2dwb ANPAurora kinase A 2.7.11.1 0.661
4qny ANPMitogen activated protein kinase, putative / 0.661
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.660
4gt3 ATPMitogen-activated protein kinase 1 2.7.11.24 0.660
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.659
3blq ATPCyclin-dependent kinase 9 2.7.11.22 0.658
3t8o ATPRhodopsin kinase / 0.658
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.658
5drd ATPAurora kinase A 2.7.11.1 0.658
2itn ANPEpidermal growth factor receptor 2.7.10.1 0.657
5dr2 ATPAurora kinase A 2.7.11.1 0.657
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.656
2if8 ADPInositol polyphosphate multikinase 2.7.1.151 0.656
2pmi AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.656
2pml ANPUncharacterized protein / 0.656
3mfu ANPPeripheral plasma membrane protein CASK 2.7.11.1 0.656
4cnf MTASpoU rRNA methylase / 0.656
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.656
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.656
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.656
4m15 ADPTyrosine-protein kinase ITK/TSK 2.7.10.2 0.655
5cno ANPEpidermal growth factor receptor 2.7.10.1 0.655
2ejz SAHDiphthine synthase / 0.654
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
1ia9 ANPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.653
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.653
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
1i58 ADPChemotaxis protein CheA 2.7.13.3 0.652
1ny3 ADPMAP kinase-activated protein kinase 2 2.7.11.1 0.652
2pyw ADPMethylthioribose kinase 2.7.1.100 0.652
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.652
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.652
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.652
5dt3 ATPAurora kinase A 2.7.11.1 0.652
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.651
3g8c ADPBiotin carboxylase 6.3.4.14 0.651
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.651
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.650
3w0n ANPHygromycin-B 4-O-kinase 2.7.1.163 0.650
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.650
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.650
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.650