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
4fu0 ADP D-alanine--D-alanine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fu0 ADPD-alanine--D-alanine ligase / 1.097
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.835
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.802
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.784
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.781
3rv4 ADPBiotin carboxylase 6.3.4.14 0.765
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.760
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.755
3r5f ATPD-alanine--D-alanine ligase / 0.749
5c1p ADPD-alanine--D-alanine ligase / 0.748
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.741
4ffl ADPUncharacterized protein / 0.738
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.737
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.736
3g8d ADPBiotin carboxylase 6.3.4.14 0.736
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.736
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.732
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.732
4ffr ATPUncharacterized protein / 0.730
2zdg ADPD-alanine--D-alanine ligase / 0.728
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.726
2vqd AP2Biotin carboxylase 6.3.4.14 0.721
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.720
4dee ADPAurora kinase A 2.7.11.1 0.720
4jlp ADPAdenylate kinase / 0.717
5dr2 ATPAurora kinase A 2.7.11.1 0.716
2j9g ADPBiotin carboxylase 6.3.4.14 0.715
3wnz ADPAlanine--anticapsin ligase / 0.714
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.714
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.714
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.713
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.710
5c1o ANPD-alanine--D-alanine ligase / 0.710
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.707
1px2 ATPSynapsin-1 / 0.705
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.705
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.705
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.704
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.704
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.699
4ffm ADPUncharacterized protein / 0.698
5dn3 ATPAurora kinase A 2.7.11.1 0.697
3wo0 ADPAlanine--anticapsin ligase / 0.696
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.693
1dv2 ATPBiotin carboxylase 6.3.4.14 0.689
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.689
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
1aux AGSSynapsin-1 / 0.687
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.686
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.685
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.685
4utd ACPAurora kinase A 2.7.11.1 0.682
5l3s GNPSignal recognition particle receptor FtsY / 0.682
2pyw ADPMethylthioribose kinase 2.7.1.100 0.681
3tw6 ADPPyruvate carboxylase / 0.681
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.681
4o1p ANPRibonuclease L / 0.680
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.679
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.678
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.677
2d1t SLULuciferin 4-monooxygenase 1.13.12.7 0.675
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.674
2fsn ADPArchaeal actin homolog / 0.674
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.674
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.671
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.669
1pk8 ATPSynapsin-1 / 0.669
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.669
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.668
4xvu ATPATPase GET3 / 0.668
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.667
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.667
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.666
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.666
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.664
2ha8 SAHProbable methyltransferase TARBP1 / 0.664
4g36 SLULuciferin 4-monooxygenase 1.13.12.7 0.664
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.663
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.662
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.662
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.661
2vuw 5IDSerine/threonine-protein kinase haspin 2.7.11.1 0.661
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.661
5dnr ATPAurora kinase A 2.7.11.1 0.661
5eg3 ACPFibroblast growth factor receptor 2 / 0.660
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.659
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
4jl8 ADPAdenylate kinase / 0.659
4jlb ADPAdenylate kinase / 0.659
4s1h ADPPyridoxal kinase, putative / 0.659
5dt4 ATPAurora kinase A 2.7.11.1 0.659
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.658
4cng SAHSpoU rRNA methylase / 0.658
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.658
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.656
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.655
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.655
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.654
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.654
4x8l AP5Adenylate kinase / 0.654
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.653
2pun ACPMethylthioribose kinase 2.7.1.100 0.652
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.652
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.651
4ix5 ANPUncharacterized protein / 0.651
5ckw ANPUncharacterized protein / 0.651
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.650
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.650
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.650
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.650