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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
2pyw ADP Methylthioribose kinase 2.7.1.100

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pyw ADPMethylthioribose kinase 2.7.1.100 1.119
2pui ADPMethylthioribose kinase 2.7.1.100 0.883
4dee ADPAurora kinase A 2.7.11.1 0.828
2pun ACPMethylthioribose kinase 2.7.1.100 0.821
2pup ADPMethylthioribose kinase 2.7.1.100 0.814
1mq4 ADPAurora kinase A 2.7.11.1 0.812
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.809
4ceg ADPAurora kinase A 2.7.11.1 0.807
2pul ACPMethylthioribose kinase 2.7.1.100 0.799
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.799
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.798
3cly ACPFibroblast growth factor receptor 2 / 0.791
2olc ADPMethylthioribose kinase 2.7.1.100 0.785
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.785
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.784
3ori AGSSerine/threonine protein kinase / 0.781
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.779
5dt3 ATPAurora kinase A 2.7.11.1 0.779
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.778
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.778
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.772
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.772
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.772
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.769
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.769
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.769
3bu5 ATPInsulin receptor 2.7.10.1 0.768
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.767
3c4w ATPRhodopsin kinase / 0.767
3c4z ADPRhodopsin kinase / 0.766
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.766
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.765
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.765
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.763
4gyi ADPUncharacterized protein / 0.763
4utd ACPAurora kinase A 2.7.11.1 0.762
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.760
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.759
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.758
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.758
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.758
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.758
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.757
3c50 ADPRhodopsin kinase / 0.757
2pz5 ACPFibroblast growth factor receptor 2 / 0.754
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.754
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.754
5dr2 ATPAurora kinase A 2.7.11.1 0.754
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.753
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.752
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.750
5dn3 ATPAurora kinase A 2.7.11.1 0.750
4ork GDPBifunctional AAC/APH 2.3.1 0.749
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.748
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.748
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.747
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.747
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.745
3t8o ATPRhodopsin kinase / 0.743
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.741
2py3 ACPFibroblast growth factor receptor 2 / 0.740
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.740
4n57 ADPAPH(2'')-Id / 0.738
5dt4 ATPAurora kinase A 2.7.11.1 0.738
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.737
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.736
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.735
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.734
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.733
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.733
2vqd AP2Biotin carboxylase 6.3.4.14 0.732
5dos ATPAurora kinase A 2.7.11.1 0.732
4ix5 ANPUncharacterized protein / 0.731
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.730
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.730
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.729
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.729
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.728
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.727
3c4x ATPRhodopsin kinase / 0.726
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.725
5eg3 ACPFibroblast growth factor receptor 2 / 0.725
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.724
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.724
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.723
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.723
5drd ATPAurora kinase A 2.7.11.1 0.723
4o4d ATPKinase / 0.722
2xan ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.721
5iqb GNPBifunctional AAC/APH 2.3.1 0.721
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.720
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.720
5iqf GDPBifunctional AAC/APH 2.3.1 0.720
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.719
4ffr ATPUncharacterized protein / 0.719
1m0w ANPGlutathione synthetase 6.3.2.3 0.718
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.718
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.718
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.718
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.717
5ce3 ADPProtein kinase YopO / 0.715
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.714
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.714
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.713
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.711
5dnr ATPAurora kinase A 2.7.11.1 0.711
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.710
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.708
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.707
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.706
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.706
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.705
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.705
5iqa GNPBifunctional AAC/APH 2.3.1 0.705
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.704
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
3orm AGSSerine/threonine protein kinase / 0.703
3tw6 ADPPyruvate carboxylase / 0.703
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.703
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.703
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.702
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.702
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.700
3qc9 ADPRhodopsin kinase / 0.700
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.699
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.699
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.698
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.697
2pzp ACPFibroblast growth factor receptor 2 / 0.697
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.697
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.695
2dwb ANPAurora kinase A 2.7.11.1 0.695
4q5h ANPProtein kinase OspG 2.7 0.695
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.694
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.694
4o4f ATPKinase / 0.694
1ol6 ATPAurora kinase A 2.7.11.1 0.693
4o4e ATPKinase / 0.693
3g8d ADPBiotin carboxylase 6.3.4.14 0.692
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.691
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.690
3wow ANPCasein kinase II subunit alpha 2.7.11.1 0.690
5byl GCPBifunctional AAC/APH 2.3.1 0.690
1u54 ACPActivated CDC42 kinase 1 / 0.687
5iqe GNPBifunctional AAC/APH 2.3.1 0.687
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.686
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.686
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.686
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.685
3tdv GDPGentamicin resistance protein / 0.685
3g8c ADPBiotin carboxylase 6.3.4.14 0.684
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.683
3nie ANPMitogen-activated protein kinase / 0.682
4ffm ADPUncharacterized protein / 0.682
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.681
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.681
4fu0 ADPD-alanine--D-alanine ligase / 0.681
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
4xlv ACPInsulin receptor 2.7.10.1 0.680
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.678
5iqd GNPBifunctional AAC/APH 2.3.1 0.678
1ir3 ANPInsulin receptor 2.7.10.1 0.677
4wh3 ATPN-acetylhexosamine 1-kinase 2.7.1.162 0.677
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
1cm8 ANPMitogen-activated protein kinase 12 / 0.676
4c3r ACPAurora kinase A 2.7.11.1 0.676
5iqi GNPBifunctional AAC/APH 2.3.1 0.676
4fl3 ANPTyrosine-protein kinase SYK 2.7.10.2 0.675
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.675
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.674
4ffl ADPUncharacterized protein / 0.674
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
3wo0 ADPAlanine--anticapsin ligase / 0.673
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.673
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.673
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.672
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.672
4fl2 ANPTyrosine-protein kinase SYK 2.7.10.2 0.672
3zfd ANPChromosome-associated kinesin KIF4 / 0.671
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.669
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.668
4uj3 GNPRas-related protein Rab-11A / 0.668
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.668
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.667
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.667
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.666
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.666
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.665
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
3llt ANPProtein serine/threonine kinase-1 / 0.665
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.664
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.663
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.662
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.662
5l8k ADPAurora kinase A 2.7.11.1 0.662
1f5n GNPGuanylate-binding protein 1 / 0.661
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.661
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.661
3tso GNPRas-related protein Rab-25 / 0.661
2j9g ADPBiotin carboxylase 6.3.4.14 0.660
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.660
3wnz ADPAlanine--anticapsin ligase / 0.660
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.660
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.659
2c2a ADPSensor histidine kinase / 0.659
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.659
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.659
3orp AGSSerine/threonine protein kinase / 0.658
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.658
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.658
4ix6 ADPUncharacterized protein / 0.657
3tdw GDPGentamicin resistance protein / 0.656
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.655
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.655
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.655
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.655
4nke IPEFarnesyl pyrophosphate synthase 2.5.1.10 0.655
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.655
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.654
1zm7 TTPDeoxynucleoside kinase / 0.654
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.654
4cki ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.654
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.653
5iqh GNPBifunctional AAC/APH 2.3.1 0.653
5l8j ADPAurora kinase A 2.7.11.1 0.653
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.652
2zdg ADPD-alanine--D-alanine ligase / 0.652
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.652
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.652
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.651
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.651
4ock ANPN-acetylhexosamine 1-kinase 2.7.1.162 0.651
5ckw ANPUncharacterized protein / 0.651
3ort AGSSerine/threonine protein kinase / 0.650
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.650
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.650