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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
1pk8 ATP Synapsin-1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1pk8 ATPSynapsin-1 / 1.152
2p0a ANPSynapsin-3 / 0.842
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.781
3tw6 ADPPyruvate carboxylase / 0.755
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.753
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.753
1aux AGSSynapsin-1 / 0.747
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.733
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.727
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.717
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.714
3wo0 ADPAlanine--anticapsin ligase / 0.712
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.709
2vqd AP2Biotin carboxylase 6.3.4.14 0.707
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.700
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.699
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.699
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.698
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.694
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
3wnz ADPAlanine--anticapsin ligase / 0.692
3g8d ADPBiotin carboxylase 6.3.4.14 0.691
3rv4 ADPBiotin carboxylase 6.3.4.14 0.691
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.691
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.690
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.690
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.687
2zdg ADPD-alanine--D-alanine ligase / 0.687
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.687
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.687
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.685
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.684
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
2pz5 ACPFibroblast growth factor receptor 2 / 0.683
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.683
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.683
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
1m0w ANPGlutathione synthetase 6.3.2.3 0.681
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.679
4zgn ATPCell division cycle protein 123 / 0.679
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.678
4zol ACPTubulin tyrosine ligase / 0.678
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.676
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.674
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.674
4ffl ADPUncharacterized protein / 0.674
4ffm ADPUncharacterized protein / 0.674
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.672
4fu0 ADPD-alanine--D-alanine ligase / 0.669
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
5bpf ADPD-alanine--D-alanine ligase / 0.669
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4jl8 ADPAdenylate kinase / 0.665
3wo1 ADPAlanine--anticapsin ligase / 0.664
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.663
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.663
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.663
1px2 ATPSynapsin-1 / 0.662
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.662
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.660
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.660
4jlb ADPAdenylate kinase / 0.659
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.658
3r5f ATPD-alanine--D-alanine ligase / 0.658
4cng SAHSpoU rRNA methylase / 0.658
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.656
4yvz 3ATDNA integrity scanning protein DisA / 0.656
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.655
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.654
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.654
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.653
5la6 ACPTubulin tyrosine ligase / 0.653
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.652
2pup ADPMethylthioribose kinase 2.7.1.100 0.652
5c1p ADPD-alanine--D-alanine ligase / 0.652
1n2e APCPantothenate synthetase 6.3.2.1 0.650
2yay DUPDUTPase / 0.650