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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
3wo1 ADP Alanine--anticapsin ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3wo1 ADPAlanine--anticapsin ligase / 1.016
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.758
3wnz ADPAlanine--anticapsin ligase / 0.754
2hgs ADPGlutathione synthetase 6.3.2.3 0.744
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.743
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.740
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.739
3wo0 ADPAlanine--anticapsin ligase / 0.734
4xlv ACPInsulin receptor 2.7.10.1 0.721
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.714
4ffl ADPUncharacterized protein / 0.706
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.697
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.695
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.688
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.686
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.685
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.682
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.682
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.682
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.682
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.680
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.679
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.679
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.679
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.679
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.679
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.678
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.678
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.678
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.675
3bu5 ATPInsulin receptor 2.7.10.1 0.675
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.675
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.674
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.672
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.672
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.672
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.671
3g8d ADPBiotin carboxylase 6.3.4.14 0.670
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.670
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.670
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.670
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
4ffr ATPUncharacterized protein / 0.668
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.667
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.667
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.667
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.666
2ejz SAHDiphthine synthase / 0.666
1pk8 ATPSynapsin-1 / 0.664
1px2 ATPSynapsin-1 / 0.664
2pui ADPMethylthioribose kinase 2.7.1.100 0.664
1m0w ANPGlutathione synthetase 6.3.2.3 0.663
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.663
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.663
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.662
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.661
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.661
4mv3 ACPBiotin carboxylase 6.3.4.14 0.661
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.660
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.660
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.659
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.659
1mq4 ADPAurora kinase A 2.7.11.1 0.658
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.658
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.658
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.658
4ckj ADNProto-oncogene tyrosine-protein kinase receptor Ret 2.7.10.1 0.657
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.657
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.656
5iqe GNPBifunctional AAC/APH 2.3.1 0.656
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.655
3ibq ATPPyridoxal kinase / 0.655
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.655
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.654
4dca ADPAminoglycoside phosphotransferase / 0.654
5dos ATPAurora kinase A 2.7.11.1 0.654
2c2a ADPSensor histidine kinase / 0.653
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.653
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.653
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.652
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.652
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.651
2olc ADPMethylthioribose kinase 2.7.1.100 0.651
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.651
4ysj ADPCalmodulin-like domain protein kinase / 0.651
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.650
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.650
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.650
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
5iqf GDPBifunctional AAC/APH 2.3.1 0.650