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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
2io8 ADP Bifunctional glutathionylspermidine synthetase/amidase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.172
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.158
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 1.061
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.934
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.912
3wnz ADPAlanine--anticapsin ligase / 0.883
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.878
4ffl ADPUncharacterized protein / 0.854
3wo0 ADPAlanine--anticapsin ligase / 0.849
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.847
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.844
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.840
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.828
5c1o ANPD-alanine--D-alanine ligase / 0.817
4ffr ATPUncharacterized protein / 0.811
2hgs ADPGlutathione synthetase 6.3.2.3 0.793
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.786
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.780
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.776
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.775
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.770
3rv4 ADPBiotin carboxylase 6.3.4.14 0.763
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.756
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.755
1pk8 ATPSynapsin-1 / 0.753
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.753
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.747
3wo1 ADPAlanine--anticapsin ligase / 0.743
3pff ADPATP-citrate synthase 2.3.3.8 0.741
3tw6 ADPPyruvate carboxylase / 0.739
5bpf ADPD-alanine--D-alanine ligase / 0.739
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.736
4ffm ADPUncharacterized protein / 0.733
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.731
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.727
2zdg ADPD-alanine--D-alanine ligase / 0.726
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
4ysj ADPCalmodulin-like domain protein kinase / 0.721
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.721
3bu5 ATPInsulin receptor 2.7.10.1 0.717
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.715
4zol ACPTubulin tyrosine ligase / 0.715
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.703
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.702
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.701
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.700
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.700
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.699
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.697
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.696
1px2 ATPSynapsin-1 / 0.696
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.695
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.695
5ce3 ADPProtein kinase YopO / 0.695
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.694
2vqd AP2Biotin carboxylase 6.3.4.14 0.691
2wq7 FADRE11660p / 0.691
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.689
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.688
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.686
4cng SAHSpoU rRNA methylase / 0.683
2pyw ADPMethylthioribose kinase 2.7.1.100 0.681
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.680
5iqh GNPBifunctional AAC/APH 2.3.1 0.680
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.679
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.679
1u54 ACPActivated CDC42 kinase 1 / 0.678
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.677
1dv2 ATPBiotin carboxylase 6.3.4.14 0.676
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
2j9g ANPBiotin carboxylase 6.3.4.14 0.676
1v3s ATPSignaling protein / 0.675
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.675
3cvu FADRE11660p / 0.674
4cnf MTASpoU rRNA methylase / 0.674
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.673
3r5f ATPD-alanine--D-alanine ligase / 0.673
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.671
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.670
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.670
4xlv ACPInsulin receptor 2.7.10.1 0.670
2p0a ANPSynapsin-3 / 0.668
5cb4 ACPTubulin tyrosine ligase / 0.668
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.667
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.667
4o4i ACPTubulin tyrosine ligase / 0.666
1aux AGSSynapsin-1 / 0.665
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.665
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.665
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.664
4mv3 ACPBiotin carboxylase 6.3.4.14 0.664
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.663
5dt3 ATPAurora kinase A 2.7.11.1 0.663
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.662
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.661
2q0g UPUPoly(A) polymerase, putative / 0.661
4rx6 ATPNitrogen regulatory PII-like protein / 0.661
5iqb GNPBifunctional AAC/APH 2.3.1 0.661
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.660
3kcc CMPcAMP-activated global transcriptional regulator CRP / 0.660
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.659
1m0w ANPGlutathione synthetase 6.3.2.3 0.658
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.658
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.657
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.657
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.656
5byl GCPBifunctional AAC/APH 2.3.1 0.656
1kh3 ANPArgininosuccinate synthase / 0.655
3cvy FADRE11660p / 0.655
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.655
4bn1 ADPAurora kinase A 2.7.11.1 0.654
4jl8 ADPAdenylate kinase / 0.654
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.653
5c1h GDUHisto-blood group ABO system transferase / 0.650