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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
2b0q ADP Aminoglycoside 3'-phosphotransferase 2.7.1.95

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 1.140
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.992
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.960
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.927
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.914
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.898
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.897
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.828
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.826
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.820
5ce3 ADPProtein kinase YopO / 0.813
1mq4 ADPAurora kinase A 2.7.11.1 0.806
3qc9 ADPRhodopsin kinase / 0.803
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.802
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.796
4ceg ADPAurora kinase A 2.7.11.1 0.795
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.793
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.789
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.786
2olc ADPMethylthioribose kinase 2.7.1.100 0.783
4dee ADPAurora kinase A 2.7.11.1 0.782
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.781
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.778
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.777
4utd ACPAurora kinase A 2.7.11.1 0.771
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.770
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.766
5iqf GDPBifunctional AAC/APH 2.3.1 0.766
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.764
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.760
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.756
2pup ADPMethylthioribose kinase 2.7.1.100 0.755
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.755
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.752
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.750
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.747
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
5dn3 ATPAurora kinase A 2.7.11.1 0.746
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.745
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.745
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.745
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.743
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.739
5iqh GNPBifunctional AAC/APH 2.3.1 0.739
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.738
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.737
5dos ATPAurora kinase A 2.7.11.1 0.737
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.736
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.736
3r5f ATPD-alanine--D-alanine ligase / 0.736
3t8o ATPRhodopsin kinase / 0.736
3c50 ADPRhodopsin kinase / 0.735
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.734
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.734
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.733
3c4z ADPRhodopsin kinase / 0.732
3wnz ADPAlanine--anticapsin ligase / 0.730
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.729
3tdw GDPGentamicin resistance protein / 0.729
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.729
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.728
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.728
2pz5 ACPFibroblast growth factor receptor 2 / 0.727
3c4w ATPRhodopsin kinase / 0.727
5byl GCPBifunctional AAC/APH 2.3.1 0.726
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.726
2pui ADPMethylthioribose kinase 2.7.1.100 0.725
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.725
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.724
2pyw ADPMethylthioribose kinase 2.7.1.100 0.724
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.724
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.723
5dt3 ATPAurora kinase A 2.7.11.1 0.723
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.722
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.720
4qny ANPMitogen activated protein kinase, putative / 0.720
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.720
2pun ACPMethylthioribose kinase 2.7.1.100 0.719
2pul ACPMethylthioribose kinase 2.7.1.100 0.717
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.716
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4ysj ADPCalmodulin-like domain protein kinase / 0.714
5iqb GNPBifunctional AAC/APH 2.3.1 0.714
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.713
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.710
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.710
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.710
2zdg ADPD-alanine--D-alanine ligase / 0.709
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4ork GDPBifunctional AAC/APH 2.3.1 0.708
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.707
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.706
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.705
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.705
4n57 ADPAPH(2'')-Id / 0.705
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.703
4bn1 ADPAurora kinase A 2.7.11.1 0.701
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.700
4c3r ACPAurora kinase A 2.7.11.1 0.699
4gyi ADPUncharacterized protein / 0.699
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.698
5dr2 ATPAurora kinase A 2.7.11.1 0.698
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.697
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.697
2dwb ANPAurora kinase A 2.7.11.1 0.696
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.695
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.694
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.693
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.693
5iqd GNPBifunctional AAC/APH 2.3.1 0.692
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.691
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.691
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.691
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.691
4o4d ATPKinase / 0.691
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.690
5eg3 ACPFibroblast growth factor receptor 2 / 0.690
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.689
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.688
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.688
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.687
5iqa GNPBifunctional AAC/APH 2.3.1 0.687
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.686
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
5iqi GNPBifunctional AAC/APH 2.3.1 0.686
1ol7 ADPAurora kinase A 2.7.11.1 0.685
3ibq ATPPyridoxal kinase / 0.685
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.685
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.684
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.683
2xs0 ANPMitogen-activated protein kinase 8 2.7.11.24 0.683
2ydo ADNAdenosine receptor A2a / 0.683
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
5dnr ATPAurora kinase A 2.7.11.1 0.683
3nie ANPMitogen-activated protein kinase / 0.682
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.682
4o1p ANPRibonuclease L / 0.682
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.681
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.681
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.681
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.681
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
2vqd AP2Biotin carboxylase 6.3.4.14 0.680
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.680
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.680
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.680
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.679
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.679
3wo1 ADPAlanine--anticapsin ligase / 0.679
4xlv ACPInsulin receptor 2.7.10.1 0.679
3tdv GDPGentamicin resistance protein / 0.678
3tw6 ADPPyruvate carboxylase / 0.678
5iqe GNPBifunctional AAC/APH 2.3.1 0.678
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.677
5l8l ADPAurora kinase A 2.7.11.1 0.677
4uhr NGIAdenosine receptor A2a / 0.677
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.676
1m0w ANPGlutathione synthetase 6.3.2.3 0.675
3pff ADPATP-citrate synthase 2.3.3.8 0.675
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.674
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.673
1ses AHXSerine--tRNA ligase 6.1.1.11 0.672
3a99 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.672
3bu5 ATPInsulin receptor 2.7.10.1 0.672
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.672
5drd ATPAurora kinase A 2.7.11.1 0.672
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.671
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.671
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.671
5dt4 ATPAurora kinase A 2.7.11.1 0.670
3c4x ATPRhodopsin kinase / 0.669
5ckw ANPUncharacterized protein / 0.669
1ol5 ADPAurora kinase A 2.7.11.1 0.668
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
5iqg GDPBifunctional AAC/APH 2.3.1 0.668
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.667
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.667
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.667
3hyo ADPPyridoxal kinase / 0.666
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.666
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.664
2pml ANPUncharacterized protein / 0.664
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.664
3keu ATPPyridoxal kinase 2.7.1.35 0.664
4ffm ADPUncharacterized protein / 0.664
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.663
5l8j ADPAurora kinase A 2.7.11.1 0.663
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.662
3qak UKAAdenosine receptor A2a / 0.662
4fhp UTPTerminal uridylyltransferase cid1 / 0.661
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4o4f ATPKinase / 0.661
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.660
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.659
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.658
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.657
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.657
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.657
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.656
3wo0 ADPAlanine--anticapsin ligase / 0.656
3bwj ARXcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.655
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.654
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.654
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.654
1ho5 ADNProtein UshA 3.1.3.5 0.653
3cly ACPFibroblast growth factor receptor 2 / 0.653
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.653
4ffr ATPUncharacterized protein / 0.653
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.653
2fsn ADPArchaeal actin homolog / 0.652
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.651
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.651
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.651
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.651
1cm8 ANPMitogen-activated protein kinase 12 / 0.650
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.650
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.650