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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
2p0a ANP Synapsin-3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2p0a ANPSynapsin-3 / 1.260
1pk8 ATPSynapsin-1 / 0.842
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.840
1px2 ATPSynapsin-1 / 0.818
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.811
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.804
3tw6 ADPPyruvate carboxylase / 0.804
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.796
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.796
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.783
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.772
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.771
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.764
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.763
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.763
4ffm ADPUncharacterized protein / 0.759
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.758
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.757
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.754
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.752
5bpf ADPD-alanine--D-alanine ligase / 0.745
1aux AGSSynapsin-1 / 0.738
4ffl ADPUncharacterized protein / 0.734
3wnz ADPAlanine--anticapsin ligase / 0.731
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.728
3dfc ANPDeath-associated protein kinase 1 2.7.11.1 0.727
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.724
3rv4 ADPBiotin carboxylase 6.3.4.14 0.716
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.715
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.712
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.711
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.711
5c1o ANPD-alanine--D-alanine ligase / 0.710
3wo0 ADPAlanine--anticapsin ligase / 0.709
4lrl DGTHD domain protein / 0.708
2zdg ADPD-alanine--D-alanine ligase / 0.707
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.707
5c1p ADPD-alanine--D-alanine ligase / 0.706
1m0w ANPGlutathione synthetase 6.3.2.3 0.701
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.701
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.698
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.698
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.697
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.689
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.689
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.689
4xlv ACPInsulin receptor 2.7.10.1 0.689
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.688
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.688
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.687
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.686
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.686
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.685
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.685
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.683
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.680
2wq7 FADRE11660p / 0.680
4qny ANPMitogen activated protein kinase, putative / 0.680
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.678
2hgs ADPGlutathione synthetase 6.3.2.3 0.677
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.677
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.675
2d1t SLULuciferin 4-monooxygenase 1.13.12.7 0.674
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.674
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.672
4ock ANPN-acetylhexosamine 1-kinase 2.7.1.162 0.672
4prv ADPDNA gyrase subunit B / 0.672
1hw5 CMPcAMP-activated global transcriptional regulator CRP / 0.671
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.670
2ydo ADNAdenosine receptor A2a / 0.670
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.670
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.670
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.668
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.668
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.667
2ikf UTPPoly(A) polymerase, putative / 0.667
1dv2 ATPBiotin carboxylase 6.3.4.14 0.666
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.666
2p2m PRXAcetyl-coenzyme A synthetase / 0.666
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.665
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.665
5ifi PRXAcetyl-coenzyme A synthetase / 0.665
2pck SAHDiphthine synthase / 0.663
4fkx CDPNucleoside diphosphate kinase / 0.662
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.662
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.661
4okk U5P3'-5' exoribonuclease MT2234.1 / 0.661
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.660
4hzf CMPcAMP-activated global transcriptional regulator CRP / 0.660
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.660
2wtk ANPSTE20-related kinase adapter protein alpha / 0.659
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.659
3r5f ATPD-alanine--D-alanine ligase / 0.659
3ryp CMPcAMP-activated global transcriptional regulator CRP / 0.659
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.659
5g53 NECAdenosine receptor A2a / 0.659
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.658
2pb4 SAHDiphthine synthase / 0.658
2pml ANPUncharacterized protein / 0.658
2pvr ANPCasein kinase II subunit alpha 2.7.11.1 0.658
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.658
4x3l MTARNA 2'-O ribose methyltransferase / 0.658
2vqd AP2Biotin carboxylase 6.3.4.14 0.657
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.657
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.657
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.657
1oqm UD2Beta-1,4-galactosyltransferase 1 / 0.656
1yro GDUBeta-1,4-galactosyltransferase 1 / 0.656
2p2j PRXAcetyl-coenzyme A synthetase / 0.656
2pup ADPMethylthioribose kinase 2.7.1.100 0.656
3ln3 NADAldo-keto reductase family 1 member C13 / 0.656
3qop CMPcAMP-activated global transcriptional regulator CRP / 0.656
3g8c ADPBiotin carboxylase 6.3.4.14 0.655
3pdn SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.655
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.655
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.654
2pbz ATPUncharacterized protein / 0.654
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.654
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.654
5cns DATRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.654
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.653
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.653
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.653
3cl1 PCGCyclic nucleotide-gated potassium channel mll3241 / 0.652
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.652
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.652
1pg3 PRXAcetyl-coenzyme A synthetase / 0.651
2e8s SAHDiphthine synthase / 0.651
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.651
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.651
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.650
4p5a FADFlavin-dependent thymidylate synthase / 0.650