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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
4o4f ATP Kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4o4f ATPKinase / 1.025
4o4e ATPKinase / 1.017
4o4d ATPKinase / 0.748
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.743
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.729
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.718
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.717
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.716
4gyi ADPUncharacterized protein / 0.716
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.715
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.715
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.710
3nie ANPMitogen-activated protein kinase / 0.710
4xlv ACPInsulin receptor 2.7.10.1 0.710
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.707
1ol6 ATPAurora kinase A 2.7.11.1 0.698
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.697
2olc ADPMethylthioribose kinase 2.7.1.100 0.697
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.697
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.696
2pyw ADPMethylthioribose kinase 2.7.1.100 0.694
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.693
2pul ACPMethylthioribose kinase 2.7.1.100 0.693
2yaa ATPDeath-associated protein kinase 2 / 0.692
3t8o ATPRhodopsin kinase / 0.691
5dn3 ATPAurora kinase A 2.7.11.1 0.690
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.689
3bu5 ATPInsulin receptor 2.7.10.1 0.689
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.689
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
4bn1 ADPAurora kinase A 2.7.11.1 0.688
4q5h ANPProtein kinase OspG 2.7 0.688
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.687
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.687
2pui ADPMethylthioribose kinase 2.7.1.100 0.687
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.686
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.686
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.685
5iqe GNPBifunctional AAC/APH 2.3.1 0.684
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.683
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.683
1ol5 ADPAurora kinase A 2.7.11.1 0.682
4qny ANPMitogen activated protein kinase, putative / 0.682
5iqa GNPBifunctional AAC/APH 2.3.1 0.681
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.680
4ffl ADPUncharacterized protein / 0.680
5iqd GNPBifunctional AAC/APH 2.3.1 0.680
4ffr ATPUncharacterized protein / 0.677
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.677
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.676
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.675
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.674
2if8 ADPInositol polyphosphate multikinase 2.7.1.151 0.674
4ceg ADPAurora kinase A 2.7.11.1 0.673
3g8c ADPBiotin carboxylase 6.3.4.14 0.672
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.671
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.670
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.668
3cly ACPFibroblast growth factor receptor 2 / 0.668
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.668
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.668
2wvj TTPThymidine kinase, cytosolic 2.7.1.21 0.667
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.667
3q5i ANPProtein kinase, putative / 0.666
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.664
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.663
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.662
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.662
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.662
4c3r ACPAurora kinase A 2.7.11.1 0.662
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.662
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.662
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.662
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.661
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.661
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.661
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.661
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.660
5bpf ADPD-alanine--D-alanine ligase / 0.660
2vqd AP2Biotin carboxylase 6.3.4.14 0.659
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.658
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.658
3llt ANPProtein serine/threonine kinase-1 / 0.658
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.658
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.656
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.656
5l8k ADPAurora kinase A 2.7.11.1 0.656
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.655
4mv3 ACPBiotin carboxylase 6.3.4.14 0.654
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.653
1ol7 ADPAurora kinase A 2.7.11.1 0.653
2jcs TTPDeoxynucleoside kinase / 0.651
5dnr ATPAurora kinase A 2.7.11.1 0.651
3c4w ATPRhodopsin kinase / 0.650
3rv4 ADPBiotin carboxylase 6.3.4.14 0.650
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.650