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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
3niz ADP Cdc2-like CDK2/CDC28 like protein kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 1.014
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.775
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.773
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.771
4o1p ANPRibonuclease L / 0.771
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.758
5dos ATPAurora kinase A 2.7.11.1 0.755
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.754
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.752
4qny ANPMitogen activated protein kinase, putative / 0.752
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.744
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.743
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.740
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.739
4ceg ADPAurora kinase A 2.7.11.1 0.739
4xlv ACPInsulin receptor 2.7.10.1 0.738
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.737
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.731
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.731
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.731
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.730
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.729
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.728
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.728
1cm8 ANPMitogen-activated protein kinase 12 / 0.724
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.718
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.717
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.717
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.715
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.715
5drd ATPAurora kinase A 2.7.11.1 0.715
5dt3 ATPAurora kinase A 2.7.11.1 0.715
4ffr ATPUncharacterized protein / 0.714
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.713
5dr2 ATPAurora kinase A 2.7.11.1 0.713
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.712
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.712
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.712
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.711
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.711
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.711
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.711
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.711
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.709
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.706
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.706
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.706
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.705
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.705
5ce3 ADPProtein kinase YopO / 0.705
3t8o ATPRhodopsin kinase / 0.704
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.703
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.702
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.701
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
3c4x ATPRhodopsin kinase / 0.696
3c50 ADPRhodopsin kinase / 0.696
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.696
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.695
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.695
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.694
4ysj ADPCalmodulin-like domain protein kinase / 0.694
5dt4 ATPAurora kinase A 2.7.11.1 0.694
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.693
5dnr ATPAurora kinase A 2.7.11.1 0.693
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.692
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
4dee ADPAurora kinase A 2.7.11.1 0.692
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
4ffl ADPUncharacterized protein / 0.689
5eg3 ACPFibroblast growth factor receptor 2 / 0.689
2pui ADPMethylthioribose kinase 2.7.1.100 0.688
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.688
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
2pml ANPUncharacterized protein / 0.687
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.685
4bn1 ADPAurora kinase A 2.7.11.1 0.685
3bu5 ATPInsulin receptor 2.7.10.1 0.683
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.683
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.682
3rv4 ADPBiotin carboxylase 6.3.4.14 0.682
5dn3 ATPAurora kinase A 2.7.11.1 0.682
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.680
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.679
2olc ADPMethylthioribose kinase 2.7.1.100 0.679
3c4z ADPRhodopsin kinase / 0.679
3a7h ATPSerine/threonine-protein kinase 24 2.7.11.1 0.676
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.676
3mfs ANPPeripheral plasma membrane protein CASK 2.7.11.1 0.675
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.673
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.673
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.673
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.672
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.671
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.671
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.670
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.670
3cly ACPFibroblast growth factor receptor 2 / 0.670
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.669
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.669
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.669
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.668
3gub GUBDeath-associated protein kinase 1 2.7.11.1 0.667
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.667
1ol5 ADPAurora kinase A 2.7.11.1 0.666
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4n57 ADPAPH(2'')-Id / 0.665
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.665
3nyn SGVG protein-coupled receptor kinase 6 2.7.11.16 0.664
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.664
1mq4 ADPAurora kinase A 2.7.11.1 0.663
3dtc VINMitogen-activated protein kinase kinase kinase 9 2.7.11.25 0.663
3pff ADPATP-citrate synthase 2.3.3.8 0.663
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.663
4utd ACPAurora kinase A 2.7.11.1 0.663
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.662
2itv ANPEpidermal growth factor receptor 2.7.10.1 0.662
2pup ADPMethylthioribose kinase 2.7.1.100 0.662
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.662
4uya AGSMitogen-activated protein kinase kinase kinase 21 2.7.11.25 0.662
2pyw ADPMethylthioribose kinase 2.7.1.100 0.661
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.660
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.659
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.659
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.659
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.659
3q5i ANPProtein kinase, putative / 0.658
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.658
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.658
3wnz ADPAlanine--anticapsin ligase / 0.658
4lv8 ADPRhoptry protein 5 C / 0.658
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.657
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.657
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.657
2pz5 ACPFibroblast growth factor receptor 2 / 0.657
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.657
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.657
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.656
3a8w ATPProtein kinase C iota type 2.7.11.13 0.656
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.656
2itn ANPEpidermal growth factor receptor 2.7.10.1 0.655
2vnw M01cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
3bwj ARXcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.654
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.654
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.654
4ffm ADPUncharacterized protein / 0.654
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.653
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.653
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.653
3nie ANPMitogen-activated protein kinase / 0.653
1u54 ACPActivated CDC42 kinase 1 / 0.652
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.652
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.652
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.651
4o4e ATPKinase / 0.651
4ork GDPBifunctional AAC/APH 2.3.1 0.651
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.650
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.650