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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
4ii5 ADP Cyclin-dependent kinase 2 2.7.11.22

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 1.041
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.906
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.846
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.841
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.840
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.824
4qny ANPMitogen activated protein kinase, putative / 0.822
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.811
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.808
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.806
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.801
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.800
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.799
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.794
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.790
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.786
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.784
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.783
5dr2 ATPAurora kinase A 2.7.11.1 0.783
1cm8 ANPMitogen-activated protein kinase 12 / 0.782
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.781
4dee ADPAurora kinase A 2.7.11.1 0.776
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.776
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.776
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.774
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.773
5dos ATPAurora kinase A 2.7.11.1 0.770
5ce3 ADPProtein kinase YopO / 0.766
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.765
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.765
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.761
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.761
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.757
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.756
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.755
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.752
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.752
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.752
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.749
3bu5 ATPInsulin receptor 2.7.10.1 0.746
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.745
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.745
4xlv ACPInsulin receptor 2.7.10.1 0.745
5dn3 ATPAurora kinase A 2.7.11.1 0.745
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.743
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.742
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.742
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.742
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.741
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.741
4ysj ADPCalmodulin-like domain protein kinase / 0.741
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.739
4ceg ADPAurora kinase A 2.7.11.1 0.738
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.738
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.738
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.736
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.733
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.732
5dt3 ATPAurora kinase A 2.7.11.1 0.732
2pyw ADPMethylthioribose kinase 2.7.1.100 0.730
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.730
4ffl ADPUncharacterized protein / 0.730
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.729
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.727
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.726
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.726
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.726
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.725
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.723
5dt4 ATPAurora kinase A 2.7.11.1 0.723
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.722
3c4z ADPRhodopsin kinase / 0.721
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.720
5drd ATPAurora kinase A 2.7.11.1 0.720
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.719
2olc ADPMethylthioribose kinase 2.7.1.100 0.719
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.717
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.714
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
2pup ADPMethylthioribose kinase 2.7.1.100 0.713
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.712
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.711
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.711
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.711
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.711
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.710
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.710
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.710
1ol5 ADPAurora kinase A 2.7.11.1 0.709
1mq4 ADPAurora kinase A 2.7.11.1 0.708
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.708
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.707
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.707
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.706
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.705
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
2pml ANPUncharacterized protein / 0.703
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.703
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.702
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.702
3qc9 ADPRhodopsin kinase / 0.702
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.702
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.702
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.702
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.701
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.701
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.701
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.701
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.700
2pz5 ACPFibroblast growth factor receptor 2 / 0.700
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.700
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.699
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.699
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.698
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.698
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.698
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.698
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.697
1ol6 ATPAurora kinase A 2.7.11.1 0.695
5eg3 ACPFibroblast growth factor receptor 2 / 0.695
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.694
4o1p ANPRibonuclease L / 0.694
3a99 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.693
3pff ADPATP-citrate synthase 2.3.3.8 0.693
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
3t8o ATPRhodopsin kinase / 0.692
4bn1 ADPAurora kinase A 2.7.11.1 0.692
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.692
1gy3 ATPCyclin-dependent kinase 2 2.7.11.22 0.691
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
4q5h ANPProtein kinase OspG 2.7 0.690
5bpf ADPD-alanine--D-alanine ligase / 0.690
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
5dnr ATPAurora kinase A 2.7.11.1 0.687
2pui ADPMethylthioribose kinase 2.7.1.100 0.686
3cly ACPFibroblast growth factor receptor 2 / 0.686
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.685
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.684
3c50 ADPRhodopsin kinase / 0.684
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.683
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.682
4ix5 ANPUncharacterized protein / 0.682
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.681
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.681
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.680
2cch ATPCyclin-dependent kinase 2 2.7.11.22 0.680
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.680
4pl3 ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.680
4utd ACPAurora kinase A 2.7.11.1 0.680
4f1m ACPProbable serine/threonine-protein kinase roco4 2.7.11.1 0.678
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.677
2dwb ANPAurora kinase A 2.7.11.1 0.676
1ol7 ADPAurora kinase A 2.7.11.1 0.675
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.675
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.674
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.674
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
2xs0 ANPMitogen-activated protein kinase 8 2.7.11.24 0.672
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.670
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.669
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.669
2dv4 SAHDiphthine synthase / 0.668
2e08 SAHDiphthine synthase / 0.668
2e16 SAHDiphthine synthase / 0.668
2egl SAHDiphthine synthase / 0.668
2yaa ATPDeath-associated protein kinase 2 / 0.668
3g8d ADPBiotin carboxylase 6.3.4.14 0.668
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.668
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.668
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
2dxx SAHDiphthine synthase / 0.667
2e07 SAHDiphthine synthase / 0.667
2e15 SAHDiphthine synthase / 0.667
2e7r SAHDiphthine synthase / 0.667
2emu SAHDiphthine synthase / 0.667
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.667
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
1fq1 ATPCyclin-dependent kinase 2 2.7.11.22 0.666
2e17 SAHDiphthine synthase / 0.666
2owk SAHDiphthine synthase / 0.666
2p6i SAHDiphthine synthase / 0.666
2p6k SAHDiphthine synthase / 0.666
2p9d SAHDiphthine synthase / 0.666
2p6l SAHDiphthine synthase / 0.665
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.665
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.664
1zy5 ANPeIF-2-alpha kinase GCN2 / 0.664
2ejk SAHDiphthine synthase / 0.664
2p5c SAHDiphthine synthase / 0.664
2pb4 SAHDiphthine synthase / 0.664
3wnz ADPAlanine--anticapsin ligase / 0.664
4c3r ACPAurora kinase A 2.7.11.1 0.664
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.664
2dsh SAHDiphthine synthase / 0.663
2dsi SAHDiphthine synthase / 0.663
2ed5 SAHDiphthine synthase / 0.663
2eh4 SAHDiphthine synthase / 0.663
2pch SAHDiphthine synthase / 0.663
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.663
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.662
2dv7 SAHDiphthine synthase / 0.662
2ek4 SAHDiphthine synthase / 0.662
2ek7 SAHDiphthine synthase / 0.662
2el3 SAHDiphthine synthase / 0.662
2p6d SAHDiphthine synthase / 0.662
2pb6 SAHDiphthine synthase / 0.662
3nie ANPMitogen-activated protein kinase / 0.662
2dsg SAHDiphthine synthase / 0.661
2en5 SAHDiphthine synthase / 0.661
2pb5 SAHDiphthine synthase / 0.661
2pck SAHDiphthine synthase / 0.661
2vqd AP2Biotin carboxylase 6.3.4.14 0.661
4lv8 ADPRhoptry protein 5 C / 0.661
2pci SAHDiphthine synthase / 0.660
2wqe ADPAurora kinase A 2.7.11.1 0.660
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.660
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.660
4fg8 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.660
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.660
4ork GDPBifunctional AAC/APH 2.3.1 0.660
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.660
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.659
1q99 ANPSerine/threonine-protein kinase SKY1 2.7.11.1 0.659
3c4w ATPRhodopsin kinase / 0.659
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.659
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.659
4n57 ADPAPH(2'')-Id / 0.659
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.658
1jst ATPCyclin-dependent kinase 2 2.7.11.22 0.658
2pul ACPMethylthioribose kinase 2.7.1.100 0.658
3wow ANPCasein kinase II subunit alpha 2.7.11.1 0.658
5iqg GDPBifunctional AAC/APH 2.3.1 0.658
2e8s SAHDiphthine synthase / 0.657
2eld SAHDiphthine synthase / 0.657
2pcg SAHDiphthine synthase / 0.657
2pwl ACPFibroblast growth factor receptor 2 / 0.657
4gyi ADPUncharacterized protein / 0.657
2egb SAHDiphthine synthase / 0.656
2pca SAHDiphthine synthase / 0.656
3r5f ATPD-alanine--D-alanine ligase / 0.656
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.656
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.656
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
2e8r SAHDiphthine synthase / 0.655
2ek2 SAHDiphthine synthase / 0.655
3rv4 ADPBiotin carboxylase 6.3.4.14 0.655
3wo0 ADPAlanine--anticapsin ligase / 0.655
5iqf GDPBifunctional AAC/APH 2.3.1 0.655
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
2dxw SAHDiphthine synthase / 0.654
2eka SAHDiphthine synthase / 0.654
2emr SAHDiphthine synthase / 0.654
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.654
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.654
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.654
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.654
2z6r SAHDiphthine synthase / 0.653
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.653
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.652
1m0w ANPGlutathione synthetase 6.3.2.3 0.652
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.652
3wo1 ADPAlanine--anticapsin ligase / 0.652
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.652
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.651
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.651
2zoq 5IDMitogen-activated protein kinase 3 2.7.11.24 0.650
4bwa N0BPyrrolysine--tRNA ligase / 0.650
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.650
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.650
5iqa GNPBifunctional AAC/APH 2.3.1 0.650