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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
1zar ADP RIO-type serine/threonine-protein kinase Rio2 2.7.11.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.958
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.822
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.792
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.792
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.790
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.777
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.772
3wnz ADPAlanine--anticapsin ligase / 0.771
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.766
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.766
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.765
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.763
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.758
4qny ANPMitogen activated protein kinase, putative / 0.758
4ysj ADPCalmodulin-like domain protein kinase / 0.757
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.754
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.753
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.753
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.752
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.748
2pup ADPMethylthioribose kinase 2.7.1.100 0.747
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.746
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.746
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.745
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.744
4ix5 ANPUncharacterized protein / 0.744
4xlv ACPInsulin receptor 2.7.10.1 0.744
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.743
5dt4 ATPAurora kinase A 2.7.11.1 0.743
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.742
2olc ADPMethylthioribose kinase 2.7.1.100 0.741
3bu5 ATPInsulin receptor 2.7.10.1 0.741
2pui ADPMethylthioribose kinase 2.7.1.100 0.740
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.740
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.738
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.738
5dos ATPAurora kinase A 2.7.11.1 0.737
3c4z ADPRhodopsin kinase / 0.736
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.735
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.735
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.735
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.733
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.732
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.732
3c50 ADPRhodopsin kinase / 0.731
4gyi ADPUncharacterized protein / 0.731
4dee ADPAurora kinase A 2.7.11.1 0.727
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.727
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.723
5dt3 ATPAurora kinase A 2.7.11.1 0.723
5dn3 ATPAurora kinase A 2.7.11.1 0.722
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.721
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.721
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.720
4utd ACPAurora kinase A 2.7.11.1 0.720
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.716
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.716
3qc9 ADPRhodopsin kinase / 0.716
4ceg ADPAurora kinase A 2.7.11.1 0.715
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.714
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.714
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.713
5drd ATPAurora kinase A 2.7.11.1 0.713
1u54 ACPActivated CDC42 kinase 1 / 0.712
2pul ACPMethylthioribose kinase 2.7.1.100 0.712
1mq4 ADPAurora kinase A 2.7.11.1 0.711
1ol6 ATPAurora kinase A 2.7.11.1 0.711
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.711
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.711
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.710
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.709
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.709
5dr2 ATPAurora kinase A 2.7.11.1 0.709
2pyw ADPMethylthioribose kinase 2.7.1.100 0.708
3cly ACPFibroblast growth factor receptor 2 / 0.708
4ffm ADPUncharacterized protein / 0.707
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.707
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.705
3t8o ATPRhodopsin kinase / 0.703
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.703
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.701
5ce3 ADPProtein kinase YopO / 0.701
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.700
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.700
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.700
5dnr ATPAurora kinase A 2.7.11.1 0.700
5iqb GNPBifunctional AAC/APH 2.3.1 0.700
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.699
5iqi GNPBifunctional AAC/APH 2.3.1 0.699
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.698
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.697
3q5i ANPProtein kinase, putative / 0.696
5iqa GNPBifunctional AAC/APH 2.3.1 0.696
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.695
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.695
2pun ACPMethylthioribose kinase 2.7.1.100 0.695
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.695
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.695
5iqe GNPBifunctional AAC/APH 2.3.1 0.694
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.693
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.693
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.693
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.693
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.693
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.692
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.692
2dwb ANPAurora kinase A 2.7.11.1 0.692
5iqh GNPBifunctional AAC/APH 2.3.1 0.692
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.690
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.690
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.689
5iqd GNPBifunctional AAC/APH 2.3.1 0.688
5l8k ADPAurora kinase A 2.7.11.1 0.688
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.687
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.687
1m0w ANPGlutathione synthetase 6.3.2.3 0.686
4c3r ACPAurora kinase A 2.7.11.1 0.686
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.685
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.684
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.684
2vqd AP2Biotin carboxylase 6.3.4.14 0.683
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.683
4ffr ATPUncharacterized protein / 0.682
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.682
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.682
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.681
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.681
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.680
3c4x ATPRhodopsin kinase / 0.678
1ol5 ADPAurora kinase A 2.7.11.1 0.677
4o4e ATPKinase / 0.677
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.677
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.676
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.676
2hgs ADPGlutathione synthetase 6.3.2.3 0.675
4o4f ATPKinase / 0.675
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.674
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.674
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
1cm8 ANPMitogen-activated protein kinase 12 / 0.672
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.672
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.672
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.671
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4q5h ANPProtein kinase OspG 2.7 0.671
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.670
4o1p ANPRibonuclease L / 0.670
2cjm ATPCyclin-dependent kinase 2 2.7.11.22 0.669
3kn5 ANPRibosomal protein S6 kinase alpha-5 2.7.11.1 0.669
4mv8 ACPBiotin carboxylase 6.3.4.14 0.669
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.669
3zxt ACPDeath-associated protein kinase 1 2.7.11.1 0.668
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.668
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.667
4n57 ADPAPH(2'')-Id / 0.667
5l8j ADPAurora kinase A 2.7.11.1 0.667
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
3wo1 ADPAlanine--anticapsin ligase / 0.666
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.665
4ffl ADPUncharacterized protein / 0.665
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.665
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.664
3rv4 ADPBiotin carboxylase 6.3.4.14 0.663
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.663
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.662
3c4w ATPRhodopsin kinase / 0.662
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.661
4mv3 ACPBiotin carboxylase 6.3.4.14 0.660
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.659
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.658
2xs0 ANPMitogen-activated protein kinase 8 2.7.11.24 0.658
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.658
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.658
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
5l8l ADPAurora kinase A 2.7.11.1 0.656
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.655
4hne ADPPhosphatidylinositol 4-kinase type 2-alpha / 0.655
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.655
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.655
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
1g9r UPFLgtC / 0.654
1ga8 UPFLgtC / 0.654
1ny3 ADPMAP kinase-activated protein kinase 2 2.7.11.1 0.654
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.654
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.654
2pz5 ACPFibroblast growth factor receptor 2 / 0.653
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.653
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.653
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.653
4bn1 ADPAurora kinase A 2.7.11.1 0.653
3r5f ATPD-alanine--D-alanine ligase / 0.652
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.651
3nie ANPMitogen-activated protein kinase / 0.651
3orm AGSSerine/threonine protein kinase / 0.651
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.650
3llt ANPProtein serine/threonine kinase-1 / 0.650
5byl GCPBifunctional AAC/APH 2.3.1 0.650