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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
2io9 ADP Bifunctional glutathionylspermidine synthetase/amidase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.216
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.158
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 1.042
3wo0 ADPAlanine--anticapsin ligase / 0.909
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.877
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.874
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.873
4ffl ADPUncharacterized protein / 0.863
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.859
3wnz ADPAlanine--anticapsin ligase / 0.855
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.840
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.838
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.823
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.814
4ffr ATPUncharacterized protein / 0.809
2p0a ANPSynapsin-3 / 0.804
2hgs ADPGlutathione synthetase 6.3.2.3 0.790
4ffm ADPUncharacterized protein / 0.785
5c1p ADPD-alanine--D-alanine ligase / 0.783
3tw6 ADPPyruvate carboxylase / 0.782
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.780
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.772
5c1o ANPD-alanine--D-alanine ligase / 0.772
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.766
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.760
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.757
5bpf ADPD-alanine--D-alanine ligase / 0.754
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.752
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.743
3rv4 ADPBiotin carboxylase 6.3.4.14 0.738
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.738
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.737
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.734
1pk8 ATPSynapsin-1 / 0.733
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.732
1px2 ATPSynapsin-1 / 0.728
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.726
4zol ACPTubulin tyrosine ligase / 0.725
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.722
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.713
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.713
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.712
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.711
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.710
5ce3 ADPProtein kinase YopO / 0.708
2vqd AP2Biotin carboxylase 6.3.4.14 0.706
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.706
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
3pff ADPATP-citrate synthase 2.3.3.8 0.703
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.703
4ysj ADPCalmodulin-like domain protein kinase / 0.702
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1m0w ANPGlutathione synthetase 6.3.2.3 0.698
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.697
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.696
2zdg ADPD-alanine--D-alanine ligase / 0.694
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.692
3cvu FADRE11660p / 0.692
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.691
1v3s ATPSignaling protein / 0.688
3mhy ATPNitrogen regulatory protein P-II 1 / 0.687
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.686
1dv2 ATPBiotin carboxylase 6.3.4.14 0.685
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.684
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.684
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.683
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.683
4lv8 ADPRhoptry protein 5 C / 0.683
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.682
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.680
4bwa N0BPyrrolysine--tRNA ligase / 0.680
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.679
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.678
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
3wo1 ADPAlanine--anticapsin ligase / 0.678
4mv3 ACPBiotin carboxylase 6.3.4.14 0.677
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.676
4cng SAHSpoU rRNA methylase / 0.676
5byl GCPBifunctional AAC/APH 2.3.1 0.676
2j9g ANPBiotin carboxylase 6.3.4.14 0.674
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.673
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.673
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
3r5f ATPD-alanine--D-alanine ligase / 0.669
4cnf MTASpoU rRNA methylase / 0.669
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.669
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.669
4fu0 ADPD-alanine--D-alanine ligase / 0.668
5dt3 ATPAurora kinase A 2.7.11.1 0.668
4o4i ACPTubulin tyrosine ligase / 0.667
4xlv ACPInsulin receptor 2.7.10.1 0.666
4rx6 ATPNitrogen regulatory PII-like protein / 0.664
4s1b 2BALmo1466 protein / 0.664
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.663
1u54 ACPActivated CDC42 kinase 1 / 0.662
2pyw ADPMethylthioribose kinase 2.7.1.100 0.662
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.662
1aux AGSSynapsin-1 / 0.661
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.660
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.660
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.659
2wq7 FADRE11660p / 0.658
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.658
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.658
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.657
2hdj NDPAldo-keto reductase family 1 member C2 / 0.657
4qbi AP5Adenylate kinase / 0.657
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.657
3gf4 UPGUDP-galactopyranose mutase 5.4.99.9 0.656
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.656
4zgn ATPCell division cycle protein 123 / 0.656
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.655
4n57 ADPAPH(2'')-Id / 0.655
3g8c ADPBiotin carboxylase 6.3.4.14 0.654
5iqb GNPBifunctional AAC/APH 2.3.1 0.654
1zrd CMPcAMP-activated global transcriptional regulator CRP / 0.653
3c4z ADPRhodopsin kinase / 0.653
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.653
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.653
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.653
4rz3 ADPSite-determining protein / 0.653
2wsi FADFAD synthase 2.7.7.2 0.652
3bu5 ATPInsulin receptor 2.7.10.1 0.652
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.652
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.652
1ia9 ANPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.651
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.650
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.650
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.650
3cly ACPFibroblast growth factor receptor 2 / 0.650
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.650
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.650