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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
3wnz ADP Alanine--anticapsin ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3wnz ADPAlanine--anticapsin ligase / 1.147
3wo0 ADPAlanine--anticapsin ligase / 1.043
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.937
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.883
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.873
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.856
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.855
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.844
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.837
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.835
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.827
2hgs ADPGlutathione synthetase 6.3.2.3 0.826
4ffr ATPUncharacterized protein / 0.826
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.801
4ffm ADPUncharacterized protein / 0.798
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.785
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.777
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.771
4ffl ADPUncharacterized protein / 0.768
5c1o ANPD-alanine--D-alanine ligase / 0.756
3wo1 ADPAlanine--anticapsin ligase / 0.754
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.752
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.750
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.742
2p0a ANPSynapsin-3 / 0.731
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.730
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.730
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.720
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.719
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.719
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.718
1px2 ATPSynapsin-1 / 0.715
3g8d ADPBiotin carboxylase 6.3.4.14 0.714
4fu0 ADPD-alanine--D-alanine ligase / 0.714
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.711
4ysj ADPCalmodulin-like domain protein kinase / 0.711
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.709
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.708
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.706
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.706
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.706
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.704
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
1m0w ANPGlutathione synthetase 6.3.2.3 0.703
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.703
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.702
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.702
4mv3 ACPBiotin carboxylase 6.3.4.14 0.702
2i8c ADPD-alanine--D-alanine ligase / 0.701
1aux AGSSynapsin-1 / 0.699
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.699
3c4z ADPRhodopsin kinase / 0.698
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.696
3rv4 ADPBiotin carboxylase 6.3.4.14 0.696
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.694
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.693
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.693
1pk8 ATPSynapsin-1 / 0.692
2zdg ADPD-alanine--D-alanine ligase / 0.692
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.691
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.691
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.690
2c2a ADPSensor histidine kinase / 0.689
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.687
4lv8 ADPRhoptry protein 5 C / 0.687
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.686
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.685
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.685
5ce3 ADPProtein kinase YopO / 0.685
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.683
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.682
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.682
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.681
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.681
4ork GDPBifunctional AAC/APH 2.3.1 0.681
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.680
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.679
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.679
4cng SAHSpoU rRNA methylase / 0.678
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.678
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.677
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.676
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.676
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.676
1ir3 ANPInsulin receptor 2.7.10.1 0.674
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.674
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.674
2j9g ANPBiotin carboxylase 6.3.4.14 0.673
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.673
3krf DSTGeranyl diphosphate synthase large subunit / 0.672
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.672
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.671
3mhy ATPNitrogen regulatory protein P-II 1 / 0.670
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.670
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.670
4n57 ADPAPH(2'')-Id / 0.669
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.668
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.668
5iqh GNPBifunctional AAC/APH 2.3.1 0.668
1i44 ACPInsulin receptor 2.7.10.1 0.667
3v0m 5GWHisto-blood group ABO system transferase / 0.667
5byl GCPBifunctional AAC/APH 2.3.1 0.666
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.665
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.664
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.663
1mq4 ADPAurora kinase A 2.7.11.1 0.663
3q5i ANPProtein kinase, putative / 0.663
3sl2 ATPSensor histidine kinase WalK / 0.663
4dee ADPAurora kinase A 2.7.11.1 0.663
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.662
4zol ACPTubulin tyrosine ligase / 0.662
5csh ATPCasein kinase II subunit alpha 2.7.11.1 0.662
2ejz SAHDiphthine synthase / 0.661
2o1o RISPutative farnesyl pyrophosphate synthase / 0.661
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.661
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
2pyw ADPMethylthioribose kinase 2.7.1.100 0.660
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.660
1w5t ADPORC1-type DNA replication protein 2 / 0.659
2ydo ADNAdenosine receptor A2a / 0.659
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3tw6 ADPPyruvate carboxylase / 0.659
1dv2 ATPBiotin carboxylase 6.3.4.14 0.658
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.658
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.658
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.658
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.657
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.656
4qny ANPMitogen activated protein kinase, putative / 0.656
1fnn ADPORC1-type DNA replication protein / 0.655
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.655
4au7 SAHHistone-lysine N-methyltransferase KMT5C 2.1.1.43 0.655
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.655
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.654
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.654
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.654
4bn1 ADPAurora kinase A 2.7.11.1 0.654
5cb4 ACPTubulin tyrosine ligase / 0.654
2pui ADPMethylthioribose kinase 2.7.1.100 0.653
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
3otx AP5Adenosine kinase, putative / 0.653
4cnf MTASpoU rRNA methylase / 0.653
3r5f ATPD-alanine--D-alanine ligase / 0.652
4ceg ADPAurora kinase A 2.7.11.1 0.652
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.651
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.651
2d1c NAPIsocitrate dehydrogenase [NADP] 1.1.1.42 0.651
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.651
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.650
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.650
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650