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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
3t9e ADP Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.138
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.078
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.065
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.993
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.980
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.963
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.945
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.880
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.859
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.856
4ffl ADPUncharacterized protein / 0.851
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.847
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.837
3wnz ADPAlanine--anticapsin ligase / 0.837
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.830
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.825
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.821
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.821
3rv4 ADPBiotin carboxylase 6.3.4.14 0.813
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.807
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.806
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.803
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.800
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.792
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.787
1px2 ATPSynapsin-1 / 0.784
4ffr ATPUncharacterized protein / 0.783
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.783
3wo0 ADPAlanine--anticapsin ligase / 0.780
5c1p ADPD-alanine--D-alanine ligase / 0.778
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.775
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.774
4ysj ADPCalmodulin-like domain protein kinase / 0.774
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.771
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.768
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.767
2zdg ADPD-alanine--D-alanine ligase / 0.766
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.763
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.762
2hgs ADPGlutathione synthetase 6.3.2.3 0.760
3bu5 ATPInsulin receptor 2.7.10.1 0.760
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.760
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.759
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.759
2p0a ANPSynapsin-3 / 0.758
4ffm ADPUncharacterized protein / 0.758
1m0w ANPGlutathione synthetase 6.3.2.3 0.757
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.757
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.756
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.756
5iqb GNPBifunctional AAC/APH 2.3.1 0.754
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.753
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.752
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.752
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.749
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.748
2pui ADPMethylthioribose kinase 2.7.1.100 0.747
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.747
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.746
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.746
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.746
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.737
4fu0 ADPD-alanine--D-alanine ligase / 0.737
5dn3 ATPAurora kinase A 2.7.11.1 0.736
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.735
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.734
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.734
4utd ACPAurora kinase A 2.7.11.1 0.732
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.732
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.731
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.731
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.729
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.729
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.728
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.728
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
5byl GCPBifunctional AAC/APH 2.3.1 0.727
5ce3 ADPProtein kinase YopO / 0.727
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
3g8d ADPBiotin carboxylase 6.3.4.14 0.725
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.725
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.724
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.724
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.724
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.723
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.723
3tw6 ADPPyruvate carboxylase / 0.722
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.720
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.720
1cm8 ANPMitogen-activated protein kinase 12 / 0.719
3tdw GDPGentamicin resistance protein / 0.719
3r5f ATPD-alanine--D-alanine ligase / 0.718
1mq4 ADPAurora kinase A 2.7.11.1 0.717
3pff ADPATP-citrate synthase 2.3.3.8 0.717
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.717
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.717
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.716
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.715
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.714
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.714
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.713
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.712
5c1o ANPD-alanine--D-alanine ligase / 0.712
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.710
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.709
3q5i ANPProtein kinase, putative / 0.707
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.706
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.706
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.705
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.705
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.704
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.703
4dee ADPAurora kinase A 2.7.11.1 0.703
4gyi ADPUncharacterized protein / 0.702
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
5iqa GNPBifunctional AAC/APH 2.3.1 0.700
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
4ehy ADPTetraacyldisaccharide 4'-kinase / 0.699
4o1p ANPRibonuclease L / 0.699
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.699
5iqd GNPBifunctional AAC/APH 2.3.1 0.698
5iqh GNPBifunctional AAC/APH 2.3.1 0.698
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.697
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.696
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.694
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.694
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.693
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.693
1aux AGSSynapsin-1 / 0.692
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.692
2j9g ADPBiotin carboxylase 6.3.4.14 0.692
4mv8 ACPBiotin carboxylase 6.3.4.14 0.692
4bwa N0BPyrrolysine--tRNA ligase / 0.691
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.691
4o4i ACPTubulin tyrosine ligase / 0.691
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
2pun ACPMethylthioribose kinase 2.7.1.100 0.690
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.690
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.690
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
4mv3 ACPBiotin carboxylase 6.3.4.14 0.688
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.687
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.687
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.687
1ia9 ANPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.686
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.684
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.684
1pk8 ATPSynapsin-1 / 0.683
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.683
2olc ADPMethylthioribose kinase 2.7.1.100 0.683
2wtk ANPSTE20-related kinase adapter protein alpha / 0.681
2ydo ADNAdenosine receptor A2a / 0.681
2vqd AP2Biotin carboxylase 6.3.4.14 0.680
3c4z ADPRhodopsin kinase / 0.680
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.680
4xlv ACPInsulin receptor 2.7.10.1 0.680
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.680
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.678
4ork GDPBifunctional AAC/APH 2.3.1 0.678
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.677
2p2m PRXAcetyl-coenzyme A synthetase / 0.677
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.677
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.677
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.676
1u54 ACPActivated CDC42 kinase 1 / 0.676
2pup ADPMethylthioribose kinase 2.7.1.100 0.676
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.675
4s1h ADPPyridoxal kinase, putative / 0.675
5iqi GNPBifunctional AAC/APH 2.3.1 0.675
1g9r UPFLgtC / 0.674
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.674
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.674
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.674
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.672
3cvu FADRE11660p / 0.672
5dr2 ATPAurora kinase A 2.7.11.1 0.672
4bw9 ANPPyrrolysine--tRNA ligase / 0.671
5drd ATPAurora kinase A 2.7.11.1 0.671
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
3wo1 ADPAlanine--anticapsin ligase / 0.670
4uhr NGIAdenosine receptor A2a / 0.670
1kh3 ANPArgininosuccinate synthase / 0.669
4ceg ADPAurora kinase A 2.7.11.1 0.669
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.668
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.667
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.666
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.666
3t7v SAM3-methylornithine synthase / 0.666
3agl A03cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4qny ANPMitogen activated protein kinase, putative / 0.665
2pml ANPUncharacterized protein / 0.664
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.664
4cng SAHSpoU rRNA methylase / 0.664
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
2pvr ANPCasein kinase II subunit alpha 2.7.11.1 0.663
5la6 ACPTubulin tyrosine ligase / 0.663
2dsi SAHDiphthine synthase / 0.662
5iqe GNPBifunctional AAC/APH 2.3.1 0.661
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.660
1zio AP5Adenylate kinase / 0.660
2p2b PRXAcetyl-coenzyme A synthetase / 0.660
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.660
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.659
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.658
3cvy FADRE11660p / 0.658
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.658
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.658
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.658
4cnf MTASpoU rRNA methylase / 0.657
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
1ga8 UPFLgtC / 0.656
4mv1 ADPBiotin carboxylase 6.3.4.14 0.656
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.656
5c1h GDUHisto-blood group ABO system transferase / 0.654
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.653
2wq7 FADRE11660p / 0.653
4n57 ADPAPH(2'')-Id / 0.653
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.653
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.652
2pyw ADPMethylthioribose kinase 2.7.1.100 0.652
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.652
3zgf IUGHisto-blood group ABO system transferase / 0.652
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.652
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.652
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.651
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.651
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.651
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.651
4qbf AP5Adenylate kinase / 0.651
5cns DATRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.651
1ss9 UPFLgtC / 0.650
4o30 SAHProbable Histone-lysine N-methyltransferase ATXR5 2.1.1.43 0.650
4o4e ATPKinase / 0.650
4uoh ADPNucleoside diphosphate kinase / 0.650
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.650
5dt3 ATPAurora kinase A 2.7.11.1 0.650