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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
2zdg ADP D-alanine--D-alanine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zdg ADPD-alanine--D-alanine ligase / 1.104
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.858
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.781
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.766
4ffl ADPUncharacterized protein / 0.759
1m0w ANPGlutathione synthetase 6.3.2.3 0.758
4ffr ATPUncharacterized protein / 0.757
3r5f ATPD-alanine--D-alanine ligase / 0.739
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.739
3tw6 ADPPyruvate carboxylase / 0.737
1px2 ATPSynapsin-1 / 0.734
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.733
4fu0 ADPD-alanine--D-alanine ligase / 0.728
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.728
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.726
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.725
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.723
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.723
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.719
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.716
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.714
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.713
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.712
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.712
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.711
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.711
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.709
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.709
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.708
2p0a ANPSynapsin-3 / 0.707
5iqb GNPBifunctional AAC/APH 2.3.1 0.707
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.706
3g8c ADPBiotin carboxylase 6.3.4.14 0.705
3rv4 ADPBiotin carboxylase 6.3.4.14 0.705
3t8o ATPRhodopsin kinase / 0.703
5c1o ANPD-alanine--D-alanine ligase / 0.703
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.702
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.702
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.701
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.698
4ffm ADPUncharacterized protein / 0.698
5ckw ANPUncharacterized protein / 0.698
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.697
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.697
5bpf ADPD-alanine--D-alanine ligase / 0.695
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.694
2pml ANPUncharacterized protein / 0.693
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.693
4lrj ANPUncharacterized protein / 0.693
3wnz ADPAlanine--anticapsin ligase / 0.692
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.692
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.691
3qc9 ADPRhodopsin kinase / 0.691
5dos ATPAurora kinase A 2.7.11.1 0.691
5dt4 ATPAurora kinase A 2.7.11.1 0.691
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
3g8d ADPBiotin carboxylase 6.3.4.14 0.689
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.689
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.688
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.687
1pk8 ATPSynapsin-1 / 0.687
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.687
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.686
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.685
3wo0 ADPAlanine--anticapsin ligase / 0.685
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.684
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.683
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.682
1u5r ATPSerine/threonine-protein kinase TAO2 2.7.11.1 0.681
2py3 ACPFibroblast growth factor receptor 2 / 0.681
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.680
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.680
2pul ACPMethylthioribose kinase 2.7.1.100 0.679
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.675
5c1p ADPD-alanine--D-alanine ligase / 0.675
1dv2 ATPBiotin carboxylase 6.3.4.14 0.674
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.674
2pun ACPMethylthioribose kinase 2.7.1.100 0.674
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.674
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.673
4aqk ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.673
4uhr NGIAdenosine receptor A2a / 0.673
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.672
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.672
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.672
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.671
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.670
5dnr ATPAurora kinase A 2.7.11.1 0.670
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.669
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.669
3c4z ADPRhodopsin kinase / 0.669
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.669
3nyn SGVG protein-coupled receptor kinase 6 2.7.11.16 0.669
4o30 SAHProbable Histone-lysine N-methyltransferase ATXR5 2.1.1.43 0.669
5eg3 ACPFibroblast growth factor receptor 2 / 0.669
4ug2 NGIAdenosine receptor A2a / 0.669
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.666
4ysj ADPCalmodulin-like domain protein kinase / 0.666
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.665
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.664
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
4mv3 ACPBiotin carboxylase 6.3.4.14 0.664
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.663
4mv1 ADPBiotin carboxylase 6.3.4.14 0.663
2olc ADPMethylthioribose kinase 2.7.1.100 0.662
4ork GDPBifunctional AAC/APH 2.3.1 0.662
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.661
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.661
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.661
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.661
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.660
4xlv ACPInsulin receptor 2.7.10.1 0.660
2vr1 ATFBiotin carboxylase 6.3.4.14 0.659
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.659
2zt5 B4PGlycine--tRNA ligase / 0.658
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.658
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.657
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
4r1l ADPPhenylacetate-coenzyme A ligase / 0.657
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.657
3cvu FADRE11660p / 0.656
3orm AGSSerine/threonine protein kinase / 0.656
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.656
2wq7 FADRE11660p / 0.655
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.654
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.654
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.654
4btj ADPTau-tubulin kinase 1 2.7.11.1 0.654
4bup SAMHistone-lysine N-methyltransferase KMT5B 2.1.1.43 0.654
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.653
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.653
2i8c ADPD-alanine--D-alanine ligase / 0.653
3cvy FADRE11660p / 0.653
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.653
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.653
2pyw ADPMethylthioribose kinase 2.7.1.100 0.652
4bga ADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases / 0.652
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.651
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.651
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.651
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.651
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.650
5dr2 ATPAurora kinase A 2.7.11.1 0.650