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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
4eoo ATP Cyclin-dependent kinase 2 2.7.11.22

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.967
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.819
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.811
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.798
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.780
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.769
3bu5 ATPInsulin receptor 2.7.10.1 0.769
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.769
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.769
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.761
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.755
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.753
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.752
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.749
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.745
5dn3 ATPAurora kinase A 2.7.11.1 0.745
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.744
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.744
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.743
3cly ACPFibroblast growth factor receptor 2 / 0.741
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.741
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.739
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.738
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.737
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.737
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.735
4qny ANPMitogen activated protein kinase, putative / 0.734
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.734
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.733
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.732
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.732
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.731
2pun ACPMethylthioribose kinase 2.7.1.100 0.731
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.731
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.727
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.727
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.727
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.724
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.724
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.721
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.721
4utd ACPAurora kinase A 2.7.11.1 0.720
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.719
4bn1 ADPAurora kinase A 2.7.11.1 0.719
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.718
4ceg ADPAurora kinase A 2.7.11.1 0.718
5dr2 ATPAurora kinase A 2.7.11.1 0.718
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.717
4q5h ANPProtein kinase OspG 2.7 0.717
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.716
3nie ANPMitogen-activated protein kinase / 0.715
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.715
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.713
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
2pzp ACPFibroblast growth factor receptor 2 / 0.712
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.712
4o1p ANPRibonuclease L / 0.712
2pyw ADPMethylthioribose kinase 2.7.1.100 0.707
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.707
1ol5 ADPAurora kinase A 2.7.11.1 0.706
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.706
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.705
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.705
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.705
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.704
5ce3 ADPProtein kinase YopO / 0.704
2pup ADPMethylthioribose kinase 2.7.1.100 0.703
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.703
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.703
2pz5 ACPFibroblast growth factor receptor 2 / 0.702
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.701
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.701
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
2olc ADPMethylthioribose kinase 2.7.1.100 0.699
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.697
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.697
5c1p ADPD-alanine--D-alanine ligase / 0.697
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.696
4xlv ACPInsulin receptor 2.7.10.1 0.696
1mq4 ADPAurora kinase A 2.7.11.1 0.695
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.695
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.694
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.694
3qc9 ADPRhodopsin kinase / 0.693
4dee ADPAurora kinase A 2.7.11.1 0.693
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.691
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.691
3q5i ANPProtein kinase, putative / 0.690
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.690
2pul ACPMethylthioribose kinase 2.7.1.100 0.689
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
5bpf ADPD-alanine--D-alanine ligase / 0.689
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.687
2py3 ACPFibroblast growth factor receptor 2 / 0.686
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.686
1ol6 ATPAurora kinase A 2.7.11.1 0.685
4o4e ATPKinase / 0.685
4o4f ATPKinase / 0.685
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.684
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.684
2pui ADPMethylthioribose kinase 2.7.1.100 0.684
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.684
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.684
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
5l8j ADPAurora kinase A 2.7.11.1 0.684
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.683
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.683
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.683
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.681
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.681
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
5dt3 ATPAurora kinase A 2.7.11.1 0.680
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.679
4ysj ADPCalmodulin-like domain protein kinase / 0.678
1gy3 ATPCyclin-dependent kinase 2 2.7.11.22 0.677
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
3fzp AGSProtein-tyrosine kinase 2-beta 2.7.10.2 0.676
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.674
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.674
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.674
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.674
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.673
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.673
4gyi ADPUncharacterized protein / 0.673
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.673
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.672
1ol7 ADPAurora kinase A 2.7.11.1 0.672
3wnz ADPAlanine--anticapsin ligase / 0.672
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.671
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.671
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.671
1i44 ACPInsulin receptor 2.7.10.1 0.670
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.669
2pml ANPUncharacterized protein / 0.669
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.669
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.669
4o4d ATPKinase / 0.669
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.669
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.668
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.668
4ffr ATPUncharacterized protein / 0.668
5iqb GNPBifunctional AAC/APH 2.3.1 0.668
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.667
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.667
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.667
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.666
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.665
5c1o ANPD-alanine--D-alanine ligase / 0.664
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.663
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.663
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.663
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.662
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
1g9r UPFLgtC / 0.661
2cch ATPCyclin-dependent kinase 2 2.7.11.22 0.661
2wtk ANPSTE20-related kinase adapter protein alpha / 0.661
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.661
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.661
5eg3 ACPFibroblast growth factor receptor 2 / 0.661
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.660
3tw6 ADPPyruvate carboxylase / 0.659
3c4w ATPRhodopsin kinase / 0.657
2acx ANPG protein-coupled receptor kinase 6 2.7.11.16 0.656
2ijm ATPFocal adhesion kinase 1 2.7.10.2 0.656
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.656
4c3r ACPAurora kinase A 2.7.11.1 0.656
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.656
3c4z ADPRhodopsin kinase / 0.655
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.655
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.655
3c4x ATPRhodopsin kinase / 0.654
3tdw GDPGentamicin resistance protein / 0.654
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.654
4dt8 ADNAPH(2'')-Id / 0.654
4fu0 ADPD-alanine--D-alanine ligase / 0.654
2yaa ATPDeath-associated protein kinase 2 / 0.653
3c50 ADPRhodopsin kinase / 0.653
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.653
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.653
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
2itx ANPEpidermal growth factor receptor 2.7.10.1 0.651
2vqd AP2Biotin carboxylase 6.3.4.14 0.651
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.651
2dwb ANPAurora kinase A 2.7.11.1 0.650
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.650
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.650
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4jrn ANPRhoptry kinase family protein / 0.650
5dnr ATPAurora kinase A 2.7.11.1 0.650