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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
4ej7 ATP Aminoglycoside 3'-phosphotransferase AphA1-IAB

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 1.103
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.897
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.881
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.870
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.868
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.838
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.821
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.798
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.786
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.783
2zdg ADPD-alanine--D-alanine ligase / 0.781
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.779
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.777
4ceg ADPAurora kinase A 2.7.11.1 0.776
5byl GCPBifunctional AAC/APH 2.3.1 0.775
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.771
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.770
2olc ADPMethylthioribose kinase 2.7.1.100 0.768
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.768
4bn1 ADPAurora kinase A 2.7.11.1 0.766
5iqh GNPBifunctional AAC/APH 2.3.1 0.762
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.761
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.761
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.759
2pul ACPMethylthioribose kinase 2.7.1.100 0.758
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.757
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.756
5iqb GNPBifunctional AAC/APH 2.3.1 0.755
2pui ADPMethylthioribose kinase 2.7.1.100 0.751
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.750
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.748
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.746
3c4w ATPRhodopsin kinase / 0.746
4dee ADPAurora kinase A 2.7.11.1 0.746
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.745
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.742
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.741
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.740
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.740
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.738
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.737
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.736
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.736
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.735
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.735
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.734
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.733
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.733
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.732
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.732
1mq4 ADPAurora kinase A 2.7.11.1 0.731
4o4d ATPKinase / 0.731
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.730
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.729
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.728
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.728
3t8o ATPRhodopsin kinase / 0.728
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.728
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
2dwb ANPAurora kinase A 2.7.11.1 0.727
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.725
3ori AGSSerine/threonine protein kinase / 0.723
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.723
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.723
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.722
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.722
2pup ADPMethylthioribose kinase 2.7.1.100 0.720
2pz5 ACPFibroblast growth factor receptor 2 / 0.720
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.718
3r5f ATPD-alanine--D-alanine ligase / 0.718
5ce3 ADPProtein kinase YopO / 0.718
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.717
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.717
3wo0 ADPAlanine--anticapsin ligase / 0.715
4n57 ADPAPH(2'')-Id / 0.715
3qc9 ADPRhodopsin kinase / 0.713
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.712
5dt3 ATPAurora kinase A 2.7.11.1 0.711
2pun ACPMethylthioribose kinase 2.7.1.100 0.710
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.707
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.707
5dr2 ATPAurora kinase A 2.7.11.1 0.707
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.704
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.703
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.703
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.702
2pml ANPUncharacterized protein / 0.702
5drd ATPAurora kinase A 2.7.11.1 0.702
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
1m0w ANPGlutathione synthetase 6.3.2.3 0.700
2py3 ACPFibroblast growth factor receptor 2 / 0.700
2pyw ADPMethylthioribose kinase 2.7.1.100 0.699
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.698
4ffl ADPUncharacterized protein / 0.698
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.697
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.697
5iqa GNPBifunctional AAC/APH 2.3.1 0.697
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.696
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.695
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
5iqe GNPBifunctional AAC/APH 2.3.1 0.694
4qny ANPMitogen activated protein kinase, putative / 0.693
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.692
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.692
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.692
5iqi GNPBifunctional AAC/APH 2.3.1 0.692
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.691
4xlv ACPInsulin receptor 2.7.10.1 0.691
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.690
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.690
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.690
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.689
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.689
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.688
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.687
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
5iqf GDPBifunctional AAC/APH 2.3.1 0.687
3hzi ATPSerine/threonine-protein kinase toxin HipA / 0.686
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.686
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.686
2pzp ACPFibroblast growth factor receptor 2 / 0.685
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.685
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.685
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.684
3nie ANPMitogen-activated protein kinase / 0.683
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.682
4gyi ADPUncharacterized protein / 0.682
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
3bu5 ATPInsulin receptor 2.7.10.1 0.679
4wh3 ATPN-acetylhexosamine 1-kinase 2.7.1.162 0.679
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.679
4tuy GTPTubulin alpha-1B chain / 0.678
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.677
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.677
4tv9 GTPTubulin alpha-1B chain / 0.677
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.677
1ol6 ATPAurora kinase A 2.7.11.1 0.676
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.676
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.674
2zgy GDPPlasmid segregation protein ParM / 0.674
3c4z ADPRhodopsin kinase / 0.674
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.674
3wo1 ADPAlanine--anticapsin ligase / 0.674
2fsn ADPArchaeal actin homolog / 0.673
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.673
5la6 GTPTubulin alpha-1B chain / 0.673
1cm8 ANPMitogen-activated protein kinase 12 / 0.672
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.672
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
3rv4 ADPBiotin carboxylase 6.3.4.14 0.672
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.672
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.671
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.671
4ehu ANP2-hydroxyisocaproyl-CoA dehydratase activator / 0.671
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.668
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.667
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.666
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.666
1ol5 ADPAurora kinase A 2.7.11.1 0.664
4c3r ACPAurora kinase A 2.7.11.1 0.664
3c50 ADPRhodopsin kinase / 0.663
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.663
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.662
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.662
4o4f ATPKinase / 0.662
3llt ANPProtein serine/threonine kinase-1 / 0.661
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.661
4o4e ATPKinase / 0.661
4ork GDPBifunctional AAC/APH 2.3.1 0.661
5dos ATPAurora kinase A 2.7.11.1 0.661
5eg3 ACPFibroblast growth factor receptor 2 / 0.661
5l8l ADPAurora kinase A 2.7.11.1 0.661
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.660
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.660
4ffr ATPUncharacterized protein / 0.658
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.658
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.658
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.657
5l3s GNPSignal recognition particle receptor FtsY / 0.656
1dv2 ATPBiotin carboxylase 6.3.4.14 0.655
1ho5 ADNProtein UshA 3.1.3.5 0.654
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.654
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.654
4jsy GTPMetallophosphoesterase / 0.654
1px2 ATPSynapsin-1 / 0.653
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.653
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.653
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.653
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.653
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.653
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.652
3ibq ATPPyridoxal kinase / 0.652
4c3p ACPAurora kinase A 2.7.11.1 0.652
5g53 NECAdenosine receptor A2a / 0.652
1u54 ACPActivated CDC42 kinase 1 / 0.651
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.651
1ir3 ANPInsulin receptor 2.7.10.1 0.650
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.650
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.650
3ort AGSSerine/threonine protein kinase / 0.650
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4ix5 ANPUncharacterized protein / 0.650
4pk4 ADPUnconventional myosin-VI / 0.650
4wbn GTPTubulin alpha-1B chain / 0.650