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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
1qmz 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
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 1.003
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.841
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.833
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.808
5dos ATPAurora kinase A 2.7.11.1 0.796
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.788
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.787
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.783
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.782
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.780
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.777
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.776
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.774
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.772
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.769
5dt4 ATPAurora kinase A 2.7.11.1 0.769
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.765
5dr2 ATPAurora kinase A 2.7.11.1 0.765
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.764
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.763
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.763
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.761
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.760
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.760
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.755
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.753
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.752
4dee ADPAurora kinase A 2.7.11.1 0.745
4qny ANPMitogen activated protein kinase, putative / 0.744
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.744
5ce3 ADPProtein kinase YopO / 0.744
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.743
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.742
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.742
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.741
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.741
4xlv ACPInsulin receptor 2.7.10.1 0.741
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.739
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.736
2olc ADPMethylthioribose kinase 2.7.1.100 0.735
5dnr ATPAurora kinase A 2.7.11.1 0.735
5dn3 ATPAurora kinase A 2.7.11.1 0.733
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.732
4utd ACPAurora kinase A 2.7.11.1 0.732
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.731
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
4ceg ADPAurora kinase A 2.7.11.1 0.730
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.729
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.728
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.728
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.728
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
4ysj ADPCalmodulin-like domain protein kinase / 0.728
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.727
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.727
1ol6 ATPAurora kinase A 2.7.11.1 0.724
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.724
1mq4 ADPAurora kinase A 2.7.11.1 0.722
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.722
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.718
5dt3 ATPAurora kinase A 2.7.11.1 0.717
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.716
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.716
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.716
2pul ACPMethylthioribose kinase 2.7.1.100 0.715
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.714
3c4z ADPRhodopsin kinase / 0.713
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.712
3bu5 ATPInsulin receptor 2.7.10.1 0.712
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.712
3nie ANPMitogen-activated protein kinase / 0.711
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.710
2pyw ADPMethylthioribose kinase 2.7.1.100 0.710
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.710
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.705
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.705
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.705
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.705
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.704
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.703
3qc9 ADPRhodopsin kinase / 0.702
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.701
2pui ADPMethylthioribose kinase 2.7.1.100 0.701
3cly ACPFibroblast growth factor receptor 2 / 0.700
4bn1 ADPAurora kinase A 2.7.11.1 0.700
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.700
3q5i ANPProtein kinase, putative / 0.698
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.697
5drd ATPAurora kinase A 2.7.11.1 0.697
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.695
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.694
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.694
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.693
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.693
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.693
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.693
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
2pz5 ACPFibroblast growth factor receptor 2 / 0.692
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.692
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.692
1cm8 ANPMitogen-activated protein kinase 12 / 0.691
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.691
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.689
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.689
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.689
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.688
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.688
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.688
2yaa ATPDeath-associated protein kinase 2 / 0.687
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.686
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.686
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.686
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.683
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.682
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
1ol5 ADPAurora kinase A 2.7.11.1 0.681
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.681
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.681
3b2t M33Fibroblast growth factor receptor 2 / 0.680
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.680
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.679
4ix5 ANPUncharacterized protein / 0.679
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.677
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.676
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.676
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.676
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.675
1ol7 ADPAurora kinase A 2.7.11.1 0.674
1zy5 ANPeIF-2-alpha kinase GCN2 / 0.674
1u54 ACPActivated CDC42 kinase 1 / 0.672
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.672
2pzp ACPFibroblast growth factor receptor 2 / 0.671
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.671
3c4w ATPRhodopsin kinase / 0.671
3kn5 ANPRibosomal protein S6 kinase alpha-5 2.7.11.1 0.671
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.670
2pwl ACPFibroblast growth factor receptor 2 / 0.670
2wtk ANPSTE20-related kinase adapter protein alpha / 0.670
3a7h ATPSerine/threonine-protein kinase 24 2.7.11.1 0.670
3r5f ATPD-alanine--D-alanine ligase / 0.670
4c3r ACPAurora kinase A 2.7.11.1 0.670
5byl GCPBifunctional AAC/APH 2.3.1 0.669
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.668
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.668
3a99 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.667
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.667
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.665
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
3nyn SGVG protein-coupled receptor kinase 6 2.7.11.16 0.663
3pff ADPATP-citrate synthase 2.3.3.8 0.663
3tw6 ADPPyruvate carboxylase / 0.663
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.663
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.663
1ir3 ANPInsulin receptor 2.7.10.1 0.662
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.662
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.662
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.661
4fu0 ADPD-alanine--D-alanine ligase / 0.661
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.660
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.660
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.660
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.660
2pup ADPMethylthioribose kinase 2.7.1.100 0.660
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.660
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.659
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.659
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.658
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.658
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.657
2ijm ATPFocal adhesion kinase 1 2.7.10.2 0.657
4bwa N0BPyrrolysine--tRNA ligase / 0.657
4dt8 ADNAPH(2'')-Id / 0.657
4o1p ANPRibonuclease L / 0.657
2dwb ANPAurora kinase A 2.7.11.1 0.656
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.656
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.656
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.656
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.656
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.655
4f1o ACPProbable serine/threonine-protein kinase roco4 2.7.11.1 0.655
3llt ANPProtein serine/threonine kinase-1 / 0.654
5eg3 ACPFibroblast growth factor receptor 2 / 0.654
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.653
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.653
3c50 ADPRhodopsin kinase / 0.652
3vjo ANPEpidermal growth factor receptor 2.7.10.1 0.652
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
5iqa GNPBifunctional AAC/APH 2.3.1 0.652
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.651
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.651
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.651
5iqh GNPBifunctional AAC/APH 2.3.1 0.651
1m0w ANPGlutathione synthetase 6.3.2.3 0.650
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.650
3wo1 ADPAlanine--anticapsin ligase / 0.650