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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
5ce3 ADP Protein kinase YopO

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5ce3 ADPProtein kinase YopO / 1.085
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.816
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.813
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.806
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.798
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.790
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.786
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.779
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.777
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.769
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.767
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.766
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.766
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.766
2pml ANPUncharacterized protein / 0.765
4qny ANPMitogen activated protein kinase, putative / 0.760
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.759
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.757
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.756
5dt3 ATPAurora kinase A 2.7.11.1 0.753
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.752
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.752
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.750
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.748
4xlv ACPInsulin receptor 2.7.10.1 0.747
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.746
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.745
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.745
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.744
5dn3 ATPAurora kinase A 2.7.11.1 0.744
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.737
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.737
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.737
4ork GDPBifunctional AAC/APH 2.3.1 0.737
1mq4 ADPAurora kinase A 2.7.11.1 0.734
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.734
4ceg ADPAurora kinase A 2.7.11.1 0.733
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.733
4utd ACPAurora kinase A 2.7.11.1 0.733
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.732
5iqf GDPBifunctional AAC/APH 2.3.1 0.732
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.731
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.730
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.730
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.730
4dee ADPAurora kinase A 2.7.11.1 0.729
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.727
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.727
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.727
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.725
2vqd AP2Biotin carboxylase 6.3.4.14 0.725
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.725
5drd ATPAurora kinase A 2.7.11.1 0.724
5iqb GNPBifunctional AAC/APH 2.3.1 0.724
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.723
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.723
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.722
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.721
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.721
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.720
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.720
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.720
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.719
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.719
5dr2 ATPAurora kinase A 2.7.11.1 0.719
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.718
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.718
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.716
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
4gyi ADPUncharacterized protein / 0.716
2pyw ADPMethylthioribose kinase 2.7.1.100 0.715
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.714
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.714
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.711
3qc9 ADPRhodopsin kinase / 0.711
3tw6 ADPPyruvate carboxylase / 0.711
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.711
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.711
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.711
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.711
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.710
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.709
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.709
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4ysj ADPCalmodulin-like domain protein kinase / 0.709
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.708
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.708
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.707
3wo0 ADPAlanine--anticapsin ligase / 0.707
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.707
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.706
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.705
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.705
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.704
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.704
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.703
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.701
3bu5 ATPInsulin receptor 2.7.10.1 0.701
5dos ATPAurora kinase A 2.7.11.1 0.701
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
1cm8 ANPMitogen-activated protein kinase 12 / 0.699
1ol5 ADPAurora kinase A 2.7.11.1 0.698
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.697
3c4z ADPRhodopsin kinase / 0.697
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.697
3cly ACPFibroblast growth factor receptor 2 / 0.696
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.696
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.695
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.695
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.694
4ffl ADPUncharacterized protein / 0.694
2pvr ANPCasein kinase II subunit alpha 2.7.11.1 0.693
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.692
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.692
3vjn ANPEpidermal growth factor receptor 2.7.10.1 0.692
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.691
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.689
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
3gub GUBDeath-associated protein kinase 1 2.7.11.1 0.686
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.686
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.686
5dt4 ATPAurora kinase A 2.7.11.1 0.686
5eg3 ACPFibroblast growth factor receptor 2 / 0.686
3wnz ADPAlanine--anticapsin ligase / 0.685
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.685
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.684
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.683
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.682
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.682
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.682
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
4ix5 ANPUncharacterized protein / 0.682
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
2dwb ANPAurora kinase A 2.7.11.1 0.680
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.680
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.680
1m0w ANPGlutathione synthetase 6.3.2.3 0.679
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.679
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.678
5iqi GNPBifunctional AAC/APH 2.3.1 0.678
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.677
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.676
4o0u ADNAurora kinase A 2.7.11.1 0.676
5ckw ANPUncharacterized protein / 0.676
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.673
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4o4e ATPKinase / 0.672
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.671
5dnr ATPAurora kinase A 2.7.11.1 0.671
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
5iqd GNPBifunctional AAC/APH 2.3.1 0.669
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
5cu6 ATPCasein kinase II subunit alpha 2.7.11.1 0.667
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.666
4o0w ADNAurora kinase A 2.7.11.1 0.666
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.665
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.664
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.663
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.663
3rv4 ADPBiotin carboxylase 6.3.4.14 0.663
4bwa N0BPyrrolysine--tRNA ligase / 0.663
2fsn ADPArchaeal actin homolog / 0.662
3c50 ADPRhodopsin kinase / 0.662
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.662
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.661
2j9g ADPBiotin carboxylase 6.3.4.14 0.661
4ix6 ADPUncharacterized protein / 0.661
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.660
3agl A03cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4n57 ADPAPH(2'')-Id / 0.660
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.659
2pui ADPMethylthioribose kinase 2.7.1.100 0.659
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.659
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.658
3sl2 ATPSensor histidine kinase WalK / 0.658
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.658
3zxt ACPDeath-associated protein kinase 1 2.7.11.1 0.658
4ffm ADPUncharacterized protein / 0.658
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.658
2py3 ACPFibroblast growth factor receptor 2 / 0.657
4u0m GTPCyclic GMP-AMP synthase / 0.657
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.657
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.656
3c4x ATPRhodopsin kinase / 0.655
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.655
4prx ADPDNA gyrase subunit B / 0.655
4xf7 ACPCarbohydrate/pyrimidine kinase, PfkB family / 0.655
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.654
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.654
3vqx BLKPyrrolysine--tRNA ligase / 0.654
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.654
4o1p ANPRibonuclease L / 0.654
4lv8 ADPRhoptry protein 5 C / 0.653
3c4w ATPRhodopsin kinase / 0.652
1qrt ATPGlutamine--tRNA ligase 6.1.1.18 0.651
1u54 ACPActivated CDC42 kinase 1 / 0.651
1ol7 ADPAurora kinase A 2.7.11.1 0.650
1qrs ATPGlutamine--tRNA ligase 6.1.1.18 0.650
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.650
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.650
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.650
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.650
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.650