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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
1z2n ADP Inositol-tetrakisphosphate 1-kinase 2.7.1.134

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 1.112
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.908
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.830
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.814
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.813
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.808
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.796
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.791
4ffl ADPUncharacterized protein / 0.788
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.786
3rv4 ADPBiotin carboxylase 6.3.4.14 0.783
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.774
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.773
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.772
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.772
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.769
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.764
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.763
4ffm ADPUncharacterized protein / 0.763
4fu0 ADPD-alanine--D-alanine ligase / 0.760
1px2 ATPSynapsin-1 / 0.751
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.751
2vqd AP2Biotin carboxylase 6.3.4.14 0.746
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.738
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.731
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.731
5ce3 ADPProtein kinase YopO / 0.731
3wnz ADPAlanine--anticapsin ligase / 0.730
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.729
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.728
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.724
1m0w ANPGlutathione synthetase 6.3.2.3 0.721
4ffr ATPUncharacterized protein / 0.721
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.718
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.716
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.715
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.715
3r5f ATPD-alanine--D-alanine ligase / 0.714
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.713
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.713
3wo0 ADPAlanine--anticapsin ligase / 0.712
2zdg ADPD-alanine--D-alanine ligase / 0.711
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.709
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.706
3pff ADPATP-citrate synthase 2.3.3.8 0.706
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.705
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.704
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.701
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.700
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.697
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.697
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.696
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.696
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.695
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.694
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
1cm8 ANPMitogen-activated protein kinase 12 / 0.691
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.690
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.690
3tw6 ADPPyruvate carboxylase / 0.689
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.689
1aux AGSSynapsin-1 / 0.688
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.688
2xul ATPNitrogen regulatory protein P-II / 0.688
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.687
1pk8 ATPSynapsin-1 / 0.687
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.687
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.687
3g8d ADPBiotin carboxylase 6.3.4.14 0.686
3cvy FADRE11660p / 0.685
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.685
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.685
3cvu FADRE11660p / 0.684
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.683
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.683
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.683
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.682
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.682
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.680
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.679
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.678
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.677
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.676
5drd ATPAurora kinase A 2.7.11.1 0.676
4zgn ATPCell division cycle protein 123 / 0.675
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.674
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.674
3g8c ADPBiotin carboxylase 6.3.4.14 0.673
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.673
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.671
4o1p ANPRibonuclease L / 0.671
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.671
4mv8 ACPBiotin carboxylase 6.3.4.14 0.670
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.669
2wq7 FADRE11660p / 0.668
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.668
2wq6 FADRE11660p / 0.667
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.667
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.667
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.667
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.667
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.666
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.666
4dee ADPAurora kinase A 2.7.11.1 0.666
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.664
4s26 SAHPhosphomethylpyrimidine synthase, chloroplastic 4.1.99.17 0.664
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.663
2pui ADPMethylthioribose kinase 2.7.1.100 0.662
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.662
1ol6 ATPAurora kinase A 2.7.11.1 0.661
2j9g ADPBiotin carboxylase 6.3.4.14 0.661
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.661
2j9g ANPBiotin carboxylase 6.3.4.14 0.660
5la6 ACPTubulin tyrosine ligase / 0.660
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.658
3wo1 ADPAlanine--anticapsin ligase / 0.658
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
3lnc 5GPGuanylate kinase / 0.657
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
1s16 ANPDNA topoisomerase 4 subunit B / 0.655
2hgs ADPGlutathione synthetase 6.3.2.3 0.655
2pyw ADPMethylthioribose kinase 2.7.1.100 0.655
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.655
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.655
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.655
4mv3 ACPBiotin carboxylase 6.3.4.14 0.655
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.655
5iqf GDPBifunctional AAC/APH 2.3.1 0.655
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.654
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.653
3g6x DGTDNA polymerase iota 2.7.7.7 0.653
4ol0 GTPGTP-binding nuclear protein Ran / 0.653
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.652
3mhy ATPNitrogen regulatory protein P-II 1 / 0.652
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.652
5l8j ADPAurora kinase A 2.7.11.1 0.651
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.650