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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
2pul ACP Methylthioribose kinase 2.7.1.100

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pul ACPMethylthioribose kinase 2.7.1.100 0.996
2pun ACPMethylthioribose kinase 2.7.1.100 0.969
2pui ADPMethylthioribose kinase 2.7.1.100 0.920
2olc ADPMethylthioribose kinase 2.7.1.100 0.909
2pup ADPMethylthioribose kinase 2.7.1.100 0.881
3t8o ATPRhodopsin kinase / 0.817
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.814
2pyw ADPMethylthioribose kinase 2.7.1.100 0.799
2py3 ACPFibroblast growth factor receptor 2 / 0.790
1mq4 ADPAurora kinase A 2.7.11.1 0.780
4ceg ADPAurora kinase A 2.7.11.1 0.779
3c4z ADPRhodopsin kinase / 0.775
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.774
3c50 ADPRhodopsin kinase / 0.772
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.769
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.767
4o4d ATPKinase / 0.764
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.763
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.762
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.760
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.759
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.758
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.758
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.754
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.751
3c4w ATPRhodopsin kinase / 0.748
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.747
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.746
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.746
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.746
3qc9 ADPRhodopsin kinase / 0.746
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.743
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
2dwb ANPAurora kinase A 2.7.11.1 0.739
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.739
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.738
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.738
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.737
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.736
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.736
2pz5 ACPFibroblast growth factor receptor 2 / 0.735
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.733
3bu5 ATPInsulin receptor 2.7.10.1 0.733
4qny ANPMitogen activated protein kinase, putative / 0.733
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.731
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.731
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.731
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.731
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.729
3nie ANPMitogen-activated protein kinase / 0.729
4dee ADPAurora kinase A 2.7.11.1 0.729
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.727
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.725
3llt ANPProtein serine/threonine kinase-1 / 0.725
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.724
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.723
4xlv ACPInsulin receptor 2.7.10.1 0.723
3c4x ATPRhodopsin kinase / 0.722
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.722
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.720
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.720
1ol6 ATPAurora kinase A 2.7.11.1 0.719
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.719
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.718
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.717
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.717
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.717
3a99 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.716
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.716
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.716
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.716
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.715
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.714
3cly ACPFibroblast growth factor receptor 2 / 0.714
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.714
5dr2 ATPAurora kinase A 2.7.11.1 0.714
4jrn ANPRhoptry kinase family protein / 0.713
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.712
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.710
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.710
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.709
4bn1 ADPAurora kinase A 2.7.11.1 0.708
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.708
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.707
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.707
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.706
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.706
5iqh GNPBifunctional AAC/APH 2.3.1 0.706
1m0w ANPGlutathione synthetase 6.3.2.3 0.703
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.703
4ork GDPBifunctional AAC/APH 2.3.1 0.702
4zgn ATPCell division cycle protein 123 / 0.702
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.702
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.701
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.700
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.700
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.700
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.700
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.700
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.697
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.696
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.696
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.694
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.693
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
4o4e ATPKinase / 0.693
4o4f ATPKinase / 0.693
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.693
2pzp ACPFibroblast growth factor receptor 2 / 0.692
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.691
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
1u54 ACPActivated CDC42 kinase 1 / 0.690
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.690
5eg3 ACPFibroblast growth factor receptor 2 / 0.690
2ijm ATPFocal adhesion kinase 1 2.7.10.2 0.689
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.689
4q5h ANPProtein kinase OspG 2.7 0.689
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
5drd ATPAurora kinase A 2.7.11.1 0.688
5l8l ADPAurora kinase A 2.7.11.1 0.688
3hyo ADPPyridoxal kinase / 0.687
4gyi ADPUncharacterized protein / 0.687
5dos ATPAurora kinase A 2.7.11.1 0.687
5l8j ADPAurora kinase A 2.7.11.1 0.687
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.686
3a7h ATPSerine/threonine-protein kinase 24 2.7.11.1 0.686
3ibq ATPPyridoxal kinase / 0.686
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.686
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.686
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.686
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.684
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.684
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.683
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.683
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.683
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.681
4utd ACPAurora kinase A 2.7.11.1 0.681
4ysj ADPCalmodulin-like domain protein kinase / 0.680
2zdg ADPD-alanine--D-alanine ligase / 0.679
3q5i ANPProtein kinase, putative / 0.679
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.678
2cjm ATPCyclin-dependent kinase 2 2.7.11.22 0.677
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.677
5dt4 ATPAurora kinase A 2.7.11.1 0.677
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.676
1jst ATPCyclin-dependent kinase 2 2.7.11.22 0.675
2pml ANPUncharacterized protein / 0.675
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.675
1ol5 ADPAurora kinase A 2.7.11.1 0.674
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.674
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.674
3vjo ANPEpidermal growth factor receptor 2.7.10.1 0.673
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
5cnn ANPEpidermal growth factor receptor 2.7.10.1 0.673
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.672
3a8w ATPProtein kinase C iota type 2.7.11.13 0.672
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4ffr ATPUncharacterized protein / 0.672
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.672
1cm8 ANPMitogen-activated protein kinase 12 / 0.671
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.671
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.671
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.671
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.670
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.668
5dt3 ATPAurora kinase A 2.7.11.1 0.668
5iqb GNPBifunctional AAC/APH 2.3.1 0.668
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.667
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.667
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.665
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.665
4c3r ACPAurora kinase A 2.7.11.1 0.664
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.662
1xjn DTPVitamin B12-dependent ribonucleotide reductase / 0.662
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.662
5dnr ATPAurora kinase A 2.7.11.1 0.662
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.661
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.661
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
2acx ANPG protein-coupled receptor kinase 6 2.7.11.16 0.660
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
3tw6 ADPPyruvate carboxylase / 0.660
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.660
3ort AGSSerine/threonine protein kinase / 0.659
4oac ADPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.659
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.659
1i44 ACPInsulin receptor 2.7.10.1 0.658
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.658
1ny3 ADPMAP kinase-activated protein kinase 2 2.7.11.1 0.658
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.658
5byl GCPBifunctional AAC/APH 2.3.1 0.658
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.656
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.656
4fg7 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.656
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.655
5dn3 ATPAurora kinase A 2.7.11.1 0.655
1ol7 ADPAurora kinase A 2.7.11.1 0.653
1z6t ADPApoptotic protease-activating factor 1 / 0.653
4ffl ADPUncharacterized protein / 0.653
3tdw GDPGentamicin resistance protein / 0.652
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.651
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
1mdl SMNMandelate racemase / 0.651
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.650
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.650
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.650
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650