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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
1l8t ADP Aminoglycoside 3'-phosphotransferase 2.7.1.95

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 1.134
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 1.007
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.992
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.967
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.939
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.935
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.870
1mq4 ADPAurora kinase A 2.7.11.1 0.850
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.834
4dee ADPAurora kinase A 2.7.11.1 0.828
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.825
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.825
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.824
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.821
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.821
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.818
4ceg ADPAurora kinase A 2.7.11.1 0.817
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.817
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.815
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.811
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.803
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.794
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.790
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.790
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.782
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.782
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.778
3c50 ADPRhodopsin kinase / 0.773
2pyw ADPMethylthioribose kinase 2.7.1.100 0.772
4gyi ADPUncharacterized protein / 0.772
5dn3 ATPAurora kinase A 2.7.11.1 0.772
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.771
2pun ACPMethylthioribose kinase 2.7.1.100 0.769
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.769
5dt3 ATPAurora kinase A 2.7.11.1 0.768
5iqh GNPBifunctional AAC/APH 2.3.1 0.767
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.766
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.764
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.763
2pui ADPMethylthioribose kinase 2.7.1.100 0.762
4utd ACPAurora kinase A 2.7.11.1 0.762
3c4z ADPRhodopsin kinase / 0.761
2pul ACPMethylthioribose kinase 2.7.1.100 0.760
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.757
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.757
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.754
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.752
5ce3 ADPProtein kinase YopO / 0.752
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.751
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.749
2olc ADPMethylthioribose kinase 2.7.1.100 0.749
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.749
3t8o ATPRhodopsin kinase / 0.749
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.748
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.748
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.745
4lv8 ADPRhoptry protein 5 C / 0.744
4ork GDPBifunctional AAC/APH 2.3.1 0.743
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.743
4ysj ADPCalmodulin-like domain protein kinase / 0.743
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.741
3rv4 ADPBiotin carboxylase 6.3.4.14 0.741
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.741
3wo0 ADPAlanine--anticapsin ligase / 0.741
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.741
3c4x ATPRhodopsin kinase / 0.738
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.738
5iqb GNPBifunctional AAC/APH 2.3.1 0.736
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.735
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.733
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.732
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.731
2pup ADPMethylthioribose kinase 2.7.1.100 0.731
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.731
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.729
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.727
3tdw GDPGentamicin resistance protein / 0.727
4ix5 ANPUncharacterized protein / 0.726
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.725
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
5drd ATPAurora kinase A 2.7.11.1 0.723
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.721
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.720
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.719
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.714
3qc9 ADPRhodopsin kinase / 0.714
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.713
5dnr ATPAurora kinase A 2.7.11.1 0.713
2p0a ANPSynapsin-3 / 0.711
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.711
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.710
4n57 ADPAPH(2'')-Id / 0.710
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.709
5dt4 ATPAurora kinase A 2.7.11.1 0.708
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.706
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.705
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.705
1m0w ANPGlutathione synthetase 6.3.2.3 0.704
2dwb ANPAurora kinase A 2.7.11.1 0.704
3pff ADPATP-citrate synthase 2.3.3.8 0.704
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
1ol7 ADPAurora kinase A 2.7.11.1 0.703
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.703
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.703
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.702
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.702
3wnz ADPAlanine--anticapsin ligase / 0.702
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.701
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.700
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.700
2ydo ADNAdenosine receptor A2a / 0.700
4ffr ATPUncharacterized protein / 0.700
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.697
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.697
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.695
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.695
3cly ACPFibroblast growth factor receptor 2 / 0.694
5byl GCPBifunctional AAC/APH 2.3.1 0.694
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.693
4qny ANPMitogen activated protein kinase, putative / 0.693
5iqd GNPBifunctional AAC/APH 2.3.1 0.693
1ol5 ADPAurora kinase A 2.7.11.1 0.692
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.692
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
4o4d ATPKinase / 0.691
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.690
3llt ANPProtein serine/threonine kinase-1 / 0.689
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.689
4bn1 ADPAurora kinase A 2.7.11.1 0.689
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.689
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
3nie ANPMitogen-activated protein kinase / 0.687
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.686
3r5f ATPD-alanine--D-alanine ligase / 0.686
4wh3 ATPN-acetylhexosamine 1-kinase 2.7.1.162 0.686
5g53 NECAdenosine receptor A2a / 0.686
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.685
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.685
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
2xs0 ANPMitogen-activated protein kinase 8 2.7.11.24 0.685
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
4xlv ACPInsulin receptor 2.7.10.1 0.684
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.683
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.683
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.682
1rfu ADPPyridoxal kinase 2.7.1.35 0.681
3c4w ATPRhodopsin kinase / 0.681
5dr2 ATPAurora kinase A 2.7.11.1 0.681
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.679
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.679
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.679
5iqa GNPBifunctional AAC/APH 2.3.1 0.679
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.678
5iqf GDPBifunctional AAC/APH 2.3.1 0.678
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.677
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.677
2pz5 ACPFibroblast growth factor receptor 2 / 0.676
2x0q ATPAlcaligin biosynthesis protein / 0.676
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.676
5dos ATPAurora kinase A 2.7.11.1 0.676
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.675
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
4ffm ADPUncharacterized protein / 0.675
5iqi GNPBifunctional AAC/APH 2.3.1 0.675
1cm8 ANPMitogen-activated protein kinase 12 / 0.674
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
5eg3 ACPFibroblast growth factor receptor 2 / 0.674
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.673
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.673
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.673
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.673
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.673
2pzp ACPFibroblast growth factor receptor 2 / 0.672
2zdg ADPD-alanine--D-alanine ligase / 0.672
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.672
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.671
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.671
4o1p ANPRibonuclease L / 0.670
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.669
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.668
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.668
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.668
5l8l ADPAurora kinase A 2.7.11.1 0.667
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.666
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.666
2zgy GDPPlasmid segregation protein ParM / 0.665
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.664
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.664
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
4ffl ADPUncharacterized protein / 0.663
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.663
1ky2 GNPGTP-binding protein YPT7 / 0.662
2vqd AP2Biotin carboxylase 6.3.4.14 0.662
3bu5 ATPInsulin receptor 2.7.10.1 0.662
3tdv GDPGentamicin resistance protein / 0.662
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.661
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.661
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.660
1pk8 ATPSynapsin-1 / 0.660
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.660
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.659
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.659
4jl8 ADPAdenylate kinase / 0.659
3ibq ATPPyridoxal kinase / 0.658
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.657
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.657
3g6w GTPUracil phosphoribosyltransferase 2.4.2.9 0.657
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.657
4ug2 NGIAdenosine receptor A2a / 0.657
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.656
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.656
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.655
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.655
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.655
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.655
2b51 UTPRNA editing complex protein MP57 / 0.654
2jlr ANPGenome polyprotein 3.4.21.91 0.654
3qak UKAAdenosine receptor A2a / 0.654
4o4f ATPKinase / 0.653
2b56 UTPRNA editing complex protein MP57 / 0.652
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.652
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.652
3keu ATPPyridoxal kinase 2.7.1.35 0.652
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.651
2hgs ADPGlutathione synthetase 6.3.2.3 0.651
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.651
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.651
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.651
4c3p ACPAurora kinase A 2.7.11.1 0.651
2py3 ACPFibroblast growth factor receptor 2 / 0.650
3vhx GTPADP-ribosylation factor 6 / 0.650