Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3r5f ATP D-alanine--D-alanine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3r5f ATPD-alanine--D-alanine ligase / 0.983
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.792
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.778
4fu0 ADPD-alanine--D-alanine ligase / 0.749
2zdg ADPD-alanine--D-alanine ligase / 0.739
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.736
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.735
4ffm ADPUncharacterized protein / 0.726
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.718
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.718
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.718
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.715
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.714
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.713
4au7 SAHHistone-lysine N-methyltransferase KMT5C 2.1.1.43 0.712
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.710
4ffl ADPUncharacterized protein / 0.710
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.703
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.700
3g8d ADPBiotin carboxylase 6.3.4.14 0.700
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.697
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.697
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.697
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.696
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.693
4ffr ATPUncharacterized protein / 0.688
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.687
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.686
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.686
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.685
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.685
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.685
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.681
2i8c ADPD-alanine--D-alanine ligase / 0.680
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.678
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.677
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.675
5dt3 ATPAurora kinase A 2.7.11.1 0.675
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.675
5drd ATPAurora kinase A 2.7.11.1 0.674
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.673
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.673
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.673
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.673
4zgn ATPCell division cycle protein 123 / 0.673
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.670
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.670
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.669
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.669
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.669
2vqd AP2Biotin carboxylase 6.3.4.14 0.668
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.666
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.664
5c1p ADPD-alanine--D-alanine ligase / 0.663
1ol7 ADPAurora kinase A 2.7.11.1 0.661
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.661
1m0w ANPGlutathione synthetase 6.3.2.3 0.659
2j9g ANPBiotin carboxylase 6.3.4.14 0.659
2p0a ANPSynapsin-3 / 0.659
3q5i ANPProtein kinase, putative / 0.659
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.659
1ol5 ADPAurora kinase A 2.7.11.1 0.658
1pk8 ATPSynapsin-1 / 0.658
4dee ADPAurora kinase A 2.7.11.1 0.656
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.656
2pup ADPMethylthioribose kinase 2.7.1.100 0.655
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.655
2zbv ADNUncharacterized protein / 0.654
5dn3 ATPAurora kinase A 2.7.11.1 0.654
5l8j ADPAurora kinase A 2.7.11.1 0.654
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.653
2olc ADPMethylthioribose kinase 2.7.1.100 0.653
3c4w ATPRhodopsin kinase / 0.653
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.653
1aux AGSSynapsin-1 / 0.652
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.652
3wnz ADPAlanine--anticapsin ligase / 0.652
4mv8 ACPBiotin carboxylase 6.3.4.14 0.652
5iqf GDPBifunctional AAC/APH 2.3.1 0.652
4qny ANPMitogen activated protein kinase, putative / 0.650
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.650