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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
3vpc ADP Glutamate--LysW ligase ArgX 6.3.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 1.040
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.796
4ffr ATPUncharacterized protein / 0.775
4ffl ADPUncharacterized protein / 0.755
3wnz ADPAlanine--anticapsin ligase / 0.752
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.750
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.744
3g8d ADPBiotin carboxylase 6.3.4.14 0.738
4fu0 ADPD-alanine--D-alanine ligase / 0.726
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.723
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.722
2pyw ADPMethylthioribose kinase 2.7.1.100 0.720
1aux AGSSynapsin-1 / 0.719
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.711
2j9g ADPBiotin carboxylase 6.3.4.14 0.707
3rv4 ADPBiotin carboxylase 6.3.4.14 0.707
2j9g ANPBiotin carboxylase 6.3.4.14 0.706
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.705
4ffm ADPUncharacterized protein / 0.703
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.697
2vqd AP2Biotin carboxylase 6.3.4.14 0.695
1mq4 ADPAurora kinase A 2.7.11.1 0.693
4dee ADPAurora kinase A 2.7.11.1 0.693
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.689
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.689
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.687
2p0a ANPSynapsin-3 / 0.686
4cng SAHSpoU rRNA methylase / 0.686
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.684
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.680
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.680
1dv2 ATPBiotin carboxylase 6.3.4.14 0.677
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.677
4mv3 ACPBiotin carboxylase 6.3.4.14 0.677
4ceg ADPAurora kinase A 2.7.11.1 0.676
2zbv ADNUncharacterized protein / 0.675
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.673
4q5h ANPProtein kinase OspG 2.7 0.673
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.672
1m0w ANPGlutathione synthetase 6.3.2.3 0.672
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.671
3t8o ATPRhodopsin kinase / 0.671
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.671
2vr1 ATFBiotin carboxylase 6.3.4.14 0.668
5dt4 ATPAurora kinase A 2.7.11.1 0.668
1px2 ATPSynapsin-1 / 0.667
2dwb ANPAurora kinase A 2.7.11.1 0.667
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.667
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.666
3wo0 ADPAlanine--anticapsin ligase / 0.666
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.665
2pun ACPMethylthioribose kinase 2.7.1.100 0.665
4ix5 ANPUncharacterized protein / 0.665
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.665
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.664
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.663
2olc ADPMethylthioribose kinase 2.7.1.100 0.663
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.662
4gt3 ATPMitogen-activated protein kinase 1 2.7.11.24 0.662
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.662
5dnr ATPAurora kinase A 2.7.11.1 0.662
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.661
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.661
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.661
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.660
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.660
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.658
5dr2 ATPAurora kinase A 2.7.11.1 0.657
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.656
3cly ACPFibroblast growth factor receptor 2 / 0.656
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.656
4cnf MTASpoU rRNA methylase / 0.656
4gyi ADPUncharacterized protein / 0.656
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.656
1pk8 ATPSynapsin-1 / 0.655
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.654
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.653
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.653
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.653
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.653
1cm8 ANPMitogen-activated protein kinase 12 / 0.652
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.652
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.651
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.651
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.651
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.650