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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
1aux AGS Synapsin-1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1aux AGSSynapsin-1 / 0.967
1px2 ATPSynapsin-1 / 0.799
1pk8 ATPSynapsin-1 / 0.747
2p0a ANPSynapsin-3 / 0.738
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.719
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.715
5bpf ADPD-alanine--D-alanine ligase / 0.714
3wnz ADPAlanine--anticapsin ligase / 0.699
5c1o ANPD-alanine--D-alanine ligase / 0.699
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.695
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.693
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.692
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.689
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.689
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.688
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.688
4fu0 ADPD-alanine--D-alanine ligase / 0.687
3rv4 ADPBiotin carboxylase 6.3.4.14 0.686
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.685
4ffl ADPUncharacterized protein / 0.682
3wo0 ADPAlanine--anticapsin ligase / 0.679
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.678
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.676
5c1p ADPD-alanine--D-alanine ligase / 0.676
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.675
2j9g ADPBiotin carboxylase 6.3.4.14 0.673
2vqd AP2Biotin carboxylase 6.3.4.14 0.672
3tw6 ADPPyruvate carboxylase / 0.671
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.667
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.666
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.665
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.664
4ffm ADPUncharacterized protein / 0.664
1dv2 ATPBiotin carboxylase 6.3.4.14 0.662
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.662
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.661
3g8d ADPBiotin carboxylase 6.3.4.14 0.661
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.658
4z17 PEPEnolase / 0.657
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.656
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.654
3dyh 721Farnesyl pyrophosphate synthase / 0.654
2v57 PRLTetR family transcriptional regulator / 0.652
3r5f ATPD-alanine--D-alanine ligase / 0.652
4mv3 ACPBiotin carboxylase 6.3.4.14 0.651
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.650