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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
4azw ATP O-antigen chain terminator bifunctional methyltransferase/kinase WbdD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 1.097
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.781
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.774
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.772
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.772
2pup ADPMethylthioribose kinase 2.7.1.100 0.768
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.759
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.757
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.745
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.740
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.739
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.736
4dee ADPAurora kinase A 2.7.11.1 0.734
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.730
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.729
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.729
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.728
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.725
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.725
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.725
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.724
5iqf GDPBifunctional AAC/APH 2.3.1 0.723
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
3c4w ATPRhodopsin kinase / 0.722
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
3bu5 ATPInsulin receptor 2.7.10.1 0.721
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.719
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.718
2pyw ADPMethylthioribose kinase 2.7.1.100 0.718
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.717
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.717
2pul ACPMethylthioribose kinase 2.7.1.100 0.716
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.715
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.715
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4c3r ACPAurora kinase A 2.7.11.1 0.714
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.713
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.712
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.712
5iqb GNPBifunctional AAC/APH 2.3.1 0.712
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.710
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.709
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.709
1m0w ANPGlutathione synthetase 6.3.2.3 0.708
2pui ADPMethylthioribose kinase 2.7.1.100 0.708
4ceg ADPAurora kinase A 2.7.11.1 0.708
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.708
3nie ANPMitogen-activated protein kinase / 0.707
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.707
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
1mq4 ADPAurora kinase A 2.7.11.1 0.706
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.706
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.705
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.703
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.703
4qny ANPMitogen activated protein kinase, putative / 0.702
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.701
1i44 ACPInsulin receptor 2.7.10.1 0.700
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.699
3qc9 ADPRhodopsin kinase / 0.699
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.698
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.698
5byl GCPBifunctional AAC/APH 2.3.1 0.698
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.697
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
3t8o ATPRhodopsin kinase / 0.696
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.696
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.696
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.695
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.694
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
2wqe ADPAurora kinase A 2.7.11.1 0.692
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.692
4n57 ADPAPH(2'')-Id / 0.691
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
4c3p ACPAurora kinase A 2.7.11.1 0.690
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.690
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.690
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.690
2pzp ACPFibroblast growth factor receptor 2 / 0.689
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.689
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.688
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.688
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.687
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.685
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.684
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.683
5dt3 ATPAurora kinase A 2.7.11.1 0.683
5dt4 ATPAurora kinase A 2.7.11.1 0.683
2ijm ATPFocal adhesion kinase 1 2.7.10.2 0.682
3wnz ADPAlanine--anticapsin ligase / 0.682
3c4z ADPRhodopsin kinase / 0.681
4xlv ACPInsulin receptor 2.7.10.1 0.681
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.679
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
5l8l ADPAurora kinase A 2.7.11.1 0.679
4utd ACPAurora kinase A 2.7.11.1 0.678
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.677
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.677
5iqh GNPBifunctional AAC/APH 2.3.1 0.676
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.675
2olc ADPMethylthioribose kinase 2.7.1.100 0.675
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.675
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.673
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.673
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.673
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.672
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.672
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.671
3cly ACPFibroblast growth factor receptor 2 / 0.671
3q5i ANPProtein kinase, putative / 0.671
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.671
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.670
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.670
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.670
4ork GDPBifunctional AAC/APH 2.3.1 0.670
4q5h ANPProtein kinase OspG 2.7 0.670
2pz5 ACPFibroblast growth factor receptor 2 / 0.669
4wh3 ATPN-acetylhexosamine 1-kinase 2.7.1.162 0.669
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.668
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.667
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.667
3t7o UPGGlycogenin-1 2.4.1.186 0.665
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.665
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.665
4ock ANPN-acetylhexosamine 1-kinase 2.7.1.162 0.665
5dos ATPAurora kinase A 2.7.11.1 0.665
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.664
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
4o4d ATPKinase / 0.664
5dn3 ATPAurora kinase A 2.7.11.1 0.664
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.663
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.663
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.663
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.662
2pun ACPMethylthioribose kinase 2.7.1.100 0.662
3tdw GDPGentamicin resistance protein / 0.662
4bn1 ADPAurora kinase A 2.7.11.1 0.662
3wo1 ADPAlanine--anticapsin ligase / 0.661
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.661
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.661
5iqa GNPBifunctional AAC/APH 2.3.1 0.661
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.660
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.660
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.660
4jrn ANPRhoptry kinase family protein / 0.659
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.659
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.659
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.658
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.658
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.658
2p0a ANPSynapsin-3 / 0.657
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.656
2wtk ANPSTE20-related kinase adapter protein alpha / 0.656
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.656
5l8j ADPAurora kinase A 2.7.11.1 0.655
1ol6 ATPAurora kinase A 2.7.11.1 0.654
2dwb ANPAurora kinase A 2.7.11.1 0.654
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.654
2zdg ADPD-alanine--D-alanine ligase / 0.654
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.654
5iqe GNPBifunctional AAC/APH 2.3.1 0.654
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.653
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.653
3c50 ADPRhodopsin kinase / 0.652
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.651
4dt8 ADNAPH(2'')-Id / 0.651
2eh2 SAHDiphthine synthase / 0.650