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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
4q4c ADP Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.106
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.078
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 1.043
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.974
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.972
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.966
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.928
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.873
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.848
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.842
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.840
3wnz ADPAlanine--anticapsin ligase / 0.835
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.823
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.813
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.794
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.791
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.787
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.778
2hgs ADPGlutathione synthetase 6.3.2.3 0.777
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.776
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.775
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.772
2p0a ANPSynapsin-3 / 0.764
3wo0 ADPAlanine--anticapsin ligase / 0.764
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.762
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.762
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.760
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.760
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.758
4ysj ADPCalmodulin-like domain protein kinase / 0.756
5c1o ANPD-alanine--D-alanine ligase / 0.756
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.753
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.752
4ffr ATPUncharacterized protein / 0.750
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.750
4ffl ADPUncharacterized protein / 0.749
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.748
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.748
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.747
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.747
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.745
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.743
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.743
4ffm ADPUncharacterized protein / 0.742
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.741
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.736
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.735
1m0w ANPGlutathione synthetase 6.3.2.3 0.733
3bu5 ATPInsulin receptor 2.7.10.1 0.732
1px2 ATPSynapsin-1 / 0.730
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.729
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.729
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
2zdg ADPD-alanine--D-alanine ligase / 0.728
5c1p ADPD-alanine--D-alanine ligase / 0.727
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.726
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.720
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.717
2vqd AP2Biotin carboxylase 6.3.4.14 0.717
3g8d ADPBiotin carboxylase 6.3.4.14 0.714
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.711
4o1p ANPRibonuclease L / 0.711
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.710
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.709
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.709
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.707
3rv4 ADPBiotin carboxylase 6.3.4.14 0.707
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.707
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.706
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.706
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.704
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.702
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.702
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.701
1mq4 ADPAurora kinase A 2.7.11.1 0.700
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.697
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.696
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.696
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
1aux AGSSynapsin-1 / 0.695
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
4ork GDPBifunctional AAC/APH 2.3.1 0.692
3q5i ANPProtein kinase, putative / 0.691
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.689
3bwj ARXcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.688
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.687
3pff ADPATP-citrate synthase 2.3.3.8 0.687
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
5ce3 ADPProtein kinase YopO / 0.685
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.684
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.684
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.683
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.683
3wo1 ADPAlanine--anticapsin ligase / 0.682
5byl GCPBifunctional AAC/APH 2.3.1 0.681
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.680
5la6 ACPTubulin tyrosine ligase / 0.680
3agl A03cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.678
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.678
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.678
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.678
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.678
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.677
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.676
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.676
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.674
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.674
4bgb ADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases / 0.674
4fu0 ADPD-alanine--D-alanine ligase / 0.674
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4mv8 ACPBiotin carboxylase 6.3.4.14 0.670
1kh3 ANPArgininosuccinate synthase / 0.669
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.669
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.669
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.668
1v3s ATPSignaling protein / 0.668
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.668
2ydo ADNAdenosine receptor A2a / 0.668
3gub GUBDeath-associated protein kinase 1 2.7.11.1 0.667
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.667
4gyi ADPUncharacterized protein / 0.667
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.666
1ss9 UPFLgtC / 0.664
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.664
3tw6 ADPPyruvate carboxylase / 0.664
5cb4 ACPTubulin tyrosine ligase / 0.664
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.663
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.662
2xul ATPNitrogen regulatory protein P-II / 0.662
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.662
5iqi GNPBifunctional AAC/APH 2.3.1 0.662
2b51 UTPRNA editing complex protein MP57 / 0.661
3hpr AP5Adenylate kinase / 0.660
4jl8 ADPAdenylate kinase / 0.660
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.659
4zol ACPTubulin tyrosine ligase / 0.659
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.658
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.658
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.657
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
5c1h GDUHisto-blood group ABO system transferase / 0.657
5iqa GNPBifunctional AAC/APH 2.3.1 0.657
5iqb GNPBifunctional AAC/APH 2.3.1 0.657
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.656
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
1i9c 5ADGlutamate mutase epsilon subunit / 0.655
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.655
1z6t ADPApoptotic protease-activating factor 1 / 0.655
4pds ANPSerine/threonine-protein kinase RAD53 2.7.12.1 0.655
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.655
1ol5 ADPAurora kinase A 2.7.11.1 0.654
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.654
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.654
4uhr NGIAdenosine receptor A2a / 0.654
1p52 ADPArginine kinase 2.7.3.3 0.652
2pyw ADPMethylthioribose kinase 2.7.1.100 0.652
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.652
3wyf GTPGTP-binding nuclear protein / 0.652
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.652
5iqe GNPBifunctional AAC/APH 2.3.1 0.652
4bfm ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.651
5bpf ADPD-alanine--D-alanine ligase / 0.651
2ddo ATPPyridoxine/pyridoxal/pyridoxamine kinase / 0.650
2q66 ATPPoly(A) polymerase 2.7.7.19 0.650
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.650
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.650