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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
2bkk ADP Aminoglycoside 3'-phosphotransferase 2.7.1.95

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 1.006
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.939
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.924
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.917
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.914
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.840
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.813
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.812
4ceg ADPAurora kinase A 2.7.11.1 0.804
4dee ADPAurora kinase A 2.7.11.1 0.801
1mq4 ADPAurora kinase A 2.7.11.1 0.791
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.784
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.779
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.777
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.776
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.775
4utd ACPAurora kinase A 2.7.11.1 0.773
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.769
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.762
3c50 ADPRhodopsin kinase / 0.760
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.758
2pyw ADPMethylthioribose kinase 2.7.1.100 0.757
2pui ADPMethylthioribose kinase 2.7.1.100 0.756
4gyi ADPUncharacterized protein / 0.751
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.749
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.747
5dn3 ATPAurora kinase A 2.7.11.1 0.747
2olc ADPMethylthioribose kinase 2.7.1.100 0.745
5dt3 ATPAurora kinase A 2.7.11.1 0.745
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.743
3bu5 ATPInsulin receptor 2.7.10.1 0.738
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.736
2pul ACPMethylthioribose kinase 2.7.1.100 0.736
2pun ACPMethylthioribose kinase 2.7.1.100 0.736
3c4z ADPRhodopsin kinase / 0.736
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.734
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.730
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.730
4ork GDPBifunctional AAC/APH 2.3.1 0.729
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.729
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.728
1ol5 ADPAurora kinase A 2.7.11.1 0.725
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.723
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.723
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.723
3qc9 ADPRhodopsin kinase / 0.722
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.722
5iqb GNPBifunctional AAC/APH 2.3.1 0.722
5ce3 ADPProtein kinase YopO / 0.720
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.719
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.718
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.718
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.717
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.714
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.714
2pup ADPMethylthioribose kinase 2.7.1.100 0.711
5iqi GNPBifunctional AAC/APH 2.3.1 0.711
4ysj ADPCalmodulin-like domain protein kinase / 0.709
4xlv ACPInsulin receptor 2.7.10.1 0.708
5dr2 ATPAurora kinase A 2.7.11.1 0.708
3cly ACPFibroblast growth factor receptor 2 / 0.705
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.705
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.704
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.704
5iqg GDPBifunctional AAC/APH 2.3.1 0.703
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.702
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.702
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.702
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.701
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
5l8k ADPAurora kinase A 2.7.11.1 0.700
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.699
3t8o ATPRhodopsin kinase / 0.699
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.698
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.698
5dt4 ATPAurora kinase A 2.7.11.1 0.697
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.696
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.695
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.695
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.695
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.695
4bn1 ADPAurora kinase A 2.7.11.1 0.694
3r5f ATPD-alanine--D-alanine ligase / 0.693
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.692
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.691
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.691
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
3llt ANPProtein serine/threonine kinase-1 / 0.690
4ix5 ANPUncharacterized protein / 0.690
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.689
5iqe GNPBifunctional AAC/APH 2.3.1 0.689
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.688
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.688
4lv8 ADPRhoptry protein 5 C / 0.688
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.688
5iqh GNPBifunctional AAC/APH 2.3.1 0.688
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.687
5iqf GDPBifunctional AAC/APH 2.3.1 0.687
3wo0 ADPAlanine--anticapsin ligase / 0.686
4fu0 ADPD-alanine--D-alanine ligase / 0.685
2vqd AP2Biotin carboxylase 6.3.4.14 0.684
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.684
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.684
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.683
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
3wnz ADPAlanine--anticapsin ligase / 0.682
5byl GCPBifunctional AAC/APH 2.3.1 0.682
2hgs ADPGlutathione synthetase 6.3.2.3 0.681
5drd ATPAurora kinase A 2.7.11.1 0.681
5iqa GNPBifunctional AAC/APH 2.3.1 0.681
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.679
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.679
2dwb ANPAurora kinase A 2.7.11.1 0.678
3g6w GTPUracil phosphoribosyltransferase 2.4.2.9 0.678
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.676
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
5dnr ATPAurora kinase A 2.7.11.1 0.676
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.675
3orm AGSSerine/threonine protein kinase / 0.674
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.674
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.673
3ori AGSSerine/threonine protein kinase / 0.673
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.672
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.672
5dos ATPAurora kinase A 2.7.11.1 0.672
1cm8 ANPMitogen-activated protein kinase 12 / 0.671
3oro AGSSerine/threonine protein kinase / 0.671
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.671
5iqd GNPBifunctional AAC/APH 2.3.1 0.671
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.670
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.670
2cl6 CAGGTPase HRas / 0.670
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.670
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.670
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.669
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.669
1m0w ANPGlutathione synthetase 6.3.2.3 0.668
4qny ANPMitogen activated protein kinase, putative / 0.668
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.667
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.666
4n57 ADPAPH(2'')-Id / 0.666
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.665
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.664
5ckw ANPUncharacterized protein / 0.664
1ol7 ADPAurora kinase A 2.7.11.1 0.663
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.663
3vhx GTPADP-ribosylation factor 6 / 0.663
4o1p ANPRibonuclease L / 0.663
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.662
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.660
1fmw ATPMyosin-2 heavy chain / 0.659
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.658
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.655
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.655
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
3m0e ATPTranscriptional regulator (NtrC family) / 0.655
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.654
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.654
3tkl GTPRas-related protein Rab-1A / 0.654
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.654
1m7b GTPRho-related GTP-binding protein RhoE / 0.653
3q5i ANPProtein kinase, putative / 0.653
3tdw GDPGentamicin resistance protein / 0.653
5l8l ADPAurora kinase A 2.7.11.1 0.653
3c4x ATPRhodopsin kinase / 0.652
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.652
1ol6 ATPAurora kinase A 2.7.11.1 0.651
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.651
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.651
4o4e ATPKinase / 0.651
5eg3 ACPFibroblast growth factor receptor 2 / 0.651
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.650
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.650