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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
4o4d ATP Kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4o4d ATPKinase / 0.954
2pz5 ACPFibroblast growth factor receptor 2 / 0.825
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.806
2py3 ACPFibroblast growth factor receptor 2 / 0.806
2pzp ACPFibroblast growth factor receptor 2 / 0.786
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.774
2pul ACPMethylthioribose kinase 2.7.1.100 0.764
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.751
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.751
2pun ACPMethylthioribose kinase 2.7.1.100 0.750
3cly ACPFibroblast growth factor receptor 2 / 0.750
4o4f ATPKinase / 0.748
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.745
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.745
5byl GCPBifunctional AAC/APH 2.3.1 0.744
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.741
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.738
5iqh GNPBifunctional AAC/APH 2.3.1 0.737
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.731
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.725
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.724
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.723
2pui ADPMethylthioribose kinase 2.7.1.100 0.722
2pyw ADPMethylthioribose kinase 2.7.1.100 0.722
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.719
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.717
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.717
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.716
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.715
1m0w ANPGlutathione synthetase 6.3.2.3 0.712
3c4x ATPRhodopsin kinase / 0.712
4bn1 ADPAurora kinase A 2.7.11.1 0.712
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.711
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.711
4ork GDPBifunctional AAC/APH 2.3.1 0.711
2qcs 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
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.710
2j9g ADPBiotin carboxylase 6.3.4.14 0.709
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.707
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.706
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.703
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
2if8 ADPInositol polyphosphate multikinase 2.7.1.151 0.698
2pup ADPMethylthioribose kinase 2.7.1.100 0.698
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.697
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.697
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.695
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.694
4gyi ADPUncharacterized protein / 0.694
3bu5 ATPInsulin receptor 2.7.10.1 0.693
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
5eg3 ACPFibroblast growth factor receptor 2 / 0.693
1mq4 ADPAurora kinase A 2.7.11.1 0.692
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.690
3orm AGSSerine/threonine protein kinase / 0.689
3rv4 ADPBiotin carboxylase 6.3.4.14 0.688
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.688
4jrn ANPRhoptry kinase family protein / 0.688
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.688
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
2vqd AP2Biotin carboxylase 6.3.4.14 0.686
3nie ANPMitogen-activated protein kinase / 0.684
3m1f ATPActin, alpha skeletal muscle / 0.683
5l8j ADPAurora kinase A 2.7.11.1 0.683
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.682
3t8o ATPRhodopsin kinase / 0.682
2olc ADPMethylthioribose kinase 2.7.1.100 0.681
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
4c3r ACPAurora kinase A 2.7.11.1 0.678
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.676
4hne ADPPhosphatidylinositol 4-kinase type 2-alpha / 0.676
4o4e ATPKinase / 0.676
5l8l ADPAurora kinase A 2.7.11.1 0.675
3c4w ATPRhodopsin kinase / 0.674
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.673
3g8c ADPBiotin carboxylase 6.3.4.14 0.673
1u54 ACPActivated CDC42 kinase 1 / 0.671
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.671
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.671
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.669
3c4z ADPRhodopsin kinase / 0.667
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.667
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
4n57 ADPAPH(2'')-Id / 0.667
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.665
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.665
3qc9 ADPRhodopsin kinase / 0.665
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.665
4xlv ACPInsulin receptor 2.7.10.1 0.665
2wtk ANPSTE20-related kinase adapter protein alpha / 0.664
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.664
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.664
5iqb GNPBifunctional AAC/APH 2.3.1 0.664
3tw6 ADPPyruvate carboxylase / 0.663
4fg7 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.663
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.662
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.662
4ceg ADPAurora kinase A 2.7.11.1 0.662
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.662
2dwb ANPAurora kinase A 2.7.11.1 0.661
2v51 ATPActin, alpha skeletal muscle / 0.661
3g8d ADPBiotin carboxylase 6.3.4.14 0.661
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.660
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.660
2itx ANPEpidermal growth factor receptor 2.7.10.1 0.660
1qz5 ATPActin, alpha skeletal muscle / 0.659
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.659
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.656
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.656
5dr2 ATPAurora kinase A 2.7.11.1 0.656
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.655
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.655
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.654
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.654
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.653
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.653
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.653
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.653
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
3llt ANPProtein serine/threonine kinase-1 / 0.652
3ori AGSSerine/threonine protein kinase / 0.652
2yaa ATPDeath-associated protein kinase 2 / 0.651
4dee ADPAurora kinase A 2.7.11.1 0.651
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.651
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.651
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.651
5iqa GNPBifunctional AAC/APH 2.3.1 0.651
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.650
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.650
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.650