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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
2r7n ADP 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.982
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.781
3rv4 ADPBiotin carboxylase 6.3.4.14 0.764
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.756
4ffm ADPUncharacterized protein / 0.754
3tw6 ADPPyruvate carboxylase / 0.750
5c1p ADPD-alanine--D-alanine ligase / 0.749
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.746
4ffl ADPUncharacterized protein / 0.746
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.744
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.740
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.735
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.734
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.727
4ffr ATPUncharacterized protein / 0.725
2p0a ANPSynapsin-3 / 0.724
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.724
2vqd AP2Biotin carboxylase 6.3.4.14 0.723
3wnz ADPAlanine--anticapsin ligase / 0.720
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.718
3r5f ATPD-alanine--D-alanine ligase / 0.718
3g8d ADPBiotin carboxylase 6.3.4.14 0.717
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.714
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.709
4fu0 ADPD-alanine--D-alanine ligase / 0.704
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.696
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.692
2j9g ADPBiotin carboxylase 6.3.4.14 0.691
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.689
1pk8 ATPSynapsin-1 / 0.685
1px2 ATPSynapsin-1 / 0.684
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.683
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.679
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.678
1v3s ATPSignaling protein / 0.677
3wo0 ADPAlanine--anticapsin ligase / 0.677
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.676
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.673
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.672
4o4f ATPKinase / 0.671
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.670
4o4e ATPKinase / 0.670
2zdg ADPD-alanine--D-alanine ligase / 0.669
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.668
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.668
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.668
2olc ADPMethylthioribose kinase 2.7.1.100 0.667
4o4i ACPTubulin tyrosine ligase / 0.667
2pyw ADPMethylthioribose kinase 2.7.1.100 0.666
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.665
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.663
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.662
3mhy ATPNitrogen regulatory protein P-II 1 / 0.661
3pnd FADFAD:protein FMN transferase / 0.660
4mv3 ACPBiotin carboxylase 6.3.4.14 0.660
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.659
4cng SAHSpoU rRNA methylase / 0.659
4mv1 ADPBiotin carboxylase 6.3.4.14 0.659
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.658
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.658
5c1o ANPD-alanine--D-alanine ligase / 0.657
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.656
2ydo ADNAdenosine receptor A2a / 0.656
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.656
4cnf MTASpoU rRNA methylase / 0.656
2wq7 FADRE11660p / 0.655
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.654
4jlb ADPAdenylate kinase / 0.653
4rx6 ATPNitrogen regulatory PII-like protein / 0.653
2xul ATPNitrogen regulatory protein P-II / 0.652
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.652
4bwx AGSPAB-dependent poly(A)-specific ribonuclease subunit pan3 / 0.652
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.651
1khz ADVADP-ribose pyrophosphatase 3.6.1.13 0.651
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.651
3cvu FADRE11660p / 0.651
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.651
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.650