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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
3i12 ADP D-alanine--D-alanine ligase A 6.3.2.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 1.054
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.916
2zdg ADPD-alanine--D-alanine ligase / 0.858
4fu0 ADPD-alanine--D-alanine ligase / 0.835
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.807
3r5f ATPD-alanine--D-alanine ligase / 0.792
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.787
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.785
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.772
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.771
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.768
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.767
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.766
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.764
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.760
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.758
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.756
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.756
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.755
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.753
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.753
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.752
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.751
1m0w ANPGlutathione synthetase 6.3.2.3 0.750
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.750
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.750
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.749
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.748
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.746
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.745
2vqd AP2Biotin carboxylase 6.3.4.14 0.744
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.744
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.744
3wnz ADPAlanine--anticapsin ligase / 0.742
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
3g8d ADPBiotin carboxylase 6.3.4.14 0.738
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.738
4ffl ADPUncharacterized protein / 0.738
4utd ACPAurora kinase A 2.7.11.1 0.735
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.733
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.733
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.733
4ffm ADPUncharacterized protein / 0.730
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.729
3tw6 ADPPyruvate carboxylase / 0.729
5dr2 ATPAurora kinase A 2.7.11.1 0.729
2p0a ANPSynapsin-3 / 0.728
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.727
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.727
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.726
4ffr ATPUncharacterized protein / 0.722
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.722
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.722
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.721
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.719
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.718
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.718
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.718
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.718
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.718
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.717
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.717
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.716
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.715
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.715
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.715
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.714
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.713
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.713
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.709
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.707
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.707
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.707
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.707
4ysj ADPCalmodulin-like domain protein kinase / 0.707
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.706
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.705
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.705
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.705
1mq4 ADPAurora kinase A 2.7.11.1 0.704
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.704
5dn3 ATPAurora kinase A 2.7.11.1 0.704
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.703
3wo0 ADPAlanine--anticapsin ligase / 0.701
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.698
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.698
2olc ADPMethylthioribose kinase 2.7.1.100 0.696
5c1p ADPD-alanine--D-alanine ligase / 0.696
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
1px2 ATPSynapsin-1 / 0.695
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.691
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.691
1pk8 ATPSynapsin-1 / 0.690
4zgn ATPCell division cycle protein 123 / 0.689
5dt4 ATPAurora kinase A 2.7.11.1 0.689
5iqb GNPBifunctional AAC/APH 2.3.1 0.689
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.687
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.686
4qny ANPMitogen activated protein kinase, putative / 0.685
4xlv ACPInsulin receptor 2.7.10.1 0.684
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.683
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.683
2pml ANPUncharacterized protein / 0.682
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.682
3rv4 ADPBiotin carboxylase 6.3.4.14 0.682
5ce3 ADPProtein kinase YopO / 0.682
4ma5 ANPN5-carboxyaminoimidazole ribonucleotide synthase / 0.681
2pui ADPMethylthioribose kinase 2.7.1.100 0.678
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
4dee ADPAurora kinase A 2.7.11.1 0.678
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.678
5c1o ANPD-alanine--D-alanine ligase / 0.678
5eg3 ACPFibroblast growth factor receptor 2 / 0.678
1hpu A12Protein UshA 3.1.3.5 0.677
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.677
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.677
1aux AGSSynapsin-1 / 0.676
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.676
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.675
3hpr AP5Adenylate kinase / 0.675
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
2p20 PRXAcetyl-coenzyme A synthetase / 0.674
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.674
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.673
4oxi GAPEnterobactin synthetase component F-related protein / 0.673
2pul ACPMethylthioribose kinase 2.7.1.100 0.671
1dv2 ATPBiotin carboxylase 6.3.4.14 0.670
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.669
3mhy ATPNitrogen regulatory protein P-II 1 / 0.669
4bw9 ANPPyrrolysine--tRNA ligase / 0.669
5ckw ANPUncharacterized protein / 0.669
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.668
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.668
4uhr NGIAdenosine receptor A2a / 0.668
2ydo ADNAdenosine receptor A2a / 0.667
4cng SAHSpoU rRNA methylase / 0.667
5byl GCPBifunctional AAC/APH 2.3.1 0.667
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.666
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.666
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
4cnf MTASpoU rRNA methylase / 0.666
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.665
2vr1 ATFBiotin carboxylase 6.3.4.14 0.665
4ceg ADPAurora kinase A 2.7.11.1 0.665
1ol5 ADPAurora kinase A 2.7.11.1 0.663
2j9g ADPBiotin carboxylase 6.3.4.14 0.663
4gyi ADPUncharacterized protein / 0.663
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.663
2i8c ADPD-alanine--D-alanine ligase / 0.662
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.662
4s26 SAHPhosphomethylpyrimidine synthase, chloroplastic 4.1.99.17 0.662
2ek2 SAHDiphthine synthase / 0.661
2pcg SAHDiphthine synthase / 0.661
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.661
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.661
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.660
2dv5 SAHDiphthine synthase / 0.660
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.660
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
2dsi SAHDiphthine synthase / 0.659
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.659
4fhp UTPTerminal uridylyltransferase cid1 / 0.659
3qak UKAAdenosine receptor A2a / 0.659
2gq2 NAPFlavin-dependent thymidylate synthase 2.1.1.148 0.658
2pun ACPMethylthioribose kinase 2.7.1.100 0.658
2zt7 ATPGlycine--tRNA ligase / 0.658
3bu5 ATPInsulin receptor 2.7.10.1 0.658
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.658
3vqx BLKPyrrolysine--tRNA ligase / 0.658
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 0.658
4r1l ADPPhenylacetate-coenzyme A ligase / 0.658
5ifi PRXAcetyl-coenzyme A synthetase / 0.658
2eh4 SAHDiphthine synthase / 0.657
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.657
2eka SAHDiphthine synthase / 0.656
2el3 SAHDiphthine synthase / 0.656
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.656
4qbf AP5Adenylate kinase / 0.656
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.656
2eeq SAHDiphthine synthase / 0.655
2p5f SAHDiphthine synthase / 0.655
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.655
3t8o ATPRhodopsin kinase / 0.655
2huq SAHDiphthine synthase / 0.654
2xul ATPNitrogen regulatory protein P-II / 0.654
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.654
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.654
1ho5 ADNProtein UshA 3.1.3.5 0.653
2emr SAHDiphthine synthase / 0.653
2p2b PRXAcetyl-coenzyme A synthetase / 0.653
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.653
1pg3 PRXAcetyl-coenzyme A synthetase / 0.652
2ejk SAHDiphthine synthase / 0.651
2eld SAHDiphthine synthase / 0.650
2pca SAHDiphthine synthase / 0.650
5f59 SAHHistone-lysine N-methyltransferase 2C 2.1.1.43 0.650