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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
1px2 ATP Synapsin-1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1px2 ATPSynapsin-1 / 1.073
2p0a ANPSynapsin-3 / 0.818
1aux AGSSynapsin-1 / 0.799
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.786
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.784
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.760
4ffm ADPUncharacterized protein / 0.759
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.751
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.748
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.748
3rv4 ADPBiotin carboxylase 6.3.4.14 0.745
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.736
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.735
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.735
2zdg ADPD-alanine--D-alanine ligase / 0.734
4ffr ATPUncharacterized protein / 0.730
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.730
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.728
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.728
4ffl ADPUncharacterized protein / 0.728
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.728
3tw6 ADPPyruvate carboxylase / 0.724
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.722
5c1p ADPD-alanine--D-alanine ligase / 0.722
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.715
3wnz ADPAlanine--anticapsin ligase / 0.715
3g8d ADPBiotin carboxylase 6.3.4.14 0.714
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.712
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.707
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.705
4fu0 ADPD-alanine--D-alanine ligase / 0.705
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.700
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.696
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.696
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.695
4ysj ADPCalmodulin-like domain protein kinase / 0.693
2vqd AP2Biotin carboxylase 6.3.4.14 0.692
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.692
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.692
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.689
5bpf ADPD-alanine--D-alanine ligase / 0.689
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.686
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.685
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.684
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.684
5c1o ANPD-alanine--D-alanine ligase / 0.684
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.683
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.683
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.681
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.680
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.678
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.676
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.671
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.670
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.670
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.668
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.668
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.668
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.667
4rx6 ATPNitrogen regulatory PII-like protein / 0.666
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.665
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.665
3wo0 ADPAlanine--anticapsin ligase / 0.665
4mv3 ACPBiotin carboxylase 6.3.4.14 0.665
3wo1 ADPAlanine--anticapsin ligase / 0.664
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.662
1pk8 ATPSynapsin-1 / 0.662
2olc ADPMethylthioribose kinase 2.7.1.100 0.662
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.662
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.662
5la6 ACPTubulin tyrosine ligase / 0.660
2hgs ADPGlutathione synthetase 6.3.2.3 0.658
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.658
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.657
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.657
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
5dt3 ATPAurora kinase A 2.7.11.1 0.657
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.656
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.655
1m0w ANPGlutathione synthetase 6.3.2.3 0.654
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.654
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.653
1dv2 ATPBiotin carboxylase 6.3.4.14 0.652
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.651
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.651
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.651