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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
3iv6 SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3iv6 SAMUncharacterized protein / 1.071
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.756
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.745
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.730
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.730
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.723
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.719
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.715
5f8f SFGPossible transcriptional regulatory protein / 0.711
4c03 SFGProtein arginine N-methyltransferase 6 / 0.709
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.706
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.703
3lcc SAHThiocyanate methyltransferase 1 / 0.701
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.700
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.700
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.699
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.698
2br5 SAHCephalosporin hydroxylase CmcI / 0.695
1boo SAHModification methylase PvuII 2.1.1.113 0.694
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.691
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.691
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.689
1eg2 MTAModification methylase RsrI 2.1.1.72 0.686
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.685
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.685
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.685
3ldg SAHUncharacterized protein / 0.685
4q7f 3D1Uncharacterized protein / 0.685
5je2 SAHMethyl transferase / 0.684
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.680
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.677
3h0v M2TS-adenosylmethionine decarboxylase proenzyme 4.1.1.50 0.676
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.675
3cx4 ADPGlycogen synthase 2.4.1.21 0.675
3lfz ADPUncharacterized protein MJ1225 / 0.674
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.673
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.673
4yac NAIC alpha-dehydrogenase / 0.673
5epe SAHUncharacterized protein / 0.672
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.670
2nv4 SAMS-adenosyl-L-methionine-binding protein AF_0241 / 0.670
2y8q ADP5'-AMP-activated protein kinase subunit gamma-1 / 0.670
3bwc SAMSpermidine synthase, putative / 0.670
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.670
2j9l ATPH(+)/Cl(-) exchange transporter 5 / 0.669
4lv5 ADPRhoptry protein 5B / 0.668
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.668
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.667
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.667
5bp9 SAHPutative methyltransferase protein / 0.666
2hms NAIKtr system potassium uptake protein A / 0.665
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.665
4e2x SAHMethyltransferase / 0.665
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.664
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.663
4rv9 SAHD-mycarose 3-C-methyltransferase / 0.663
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.662
3tos SAHCalS11 / 0.662
4c05 SAHProtein arginine N-methyltransferase 6 / 0.662
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.660
4nec SAHPutative SAM-dependent methyltransferase / 0.660
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.659
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.659
3ldf SAHUncharacterized protein / 0.659
4gbe SAHDNA adenine methylase 2.1.1.72 0.659
4j36 FADKynurenine 3-monooxygenase / 0.658
4oa5 SAHO-methyltransferase family protein / 0.658
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.658
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.657
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.656
3rfx NADUronate dehydrogenase / 0.656
3emd SFGMethyltransferase / 0.655
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.655
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
1f3l SAHProtein arginine N-methyltransferase 3 / 0.653
3zc3 NAPFerredoxin--NADP reductase 1.18.1.2 0.653
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.653
1wy7 SAHUncharacterized protein / 0.652
2jcs TTPDeoxynucleoside kinase / 0.652
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.651
3rw9 DSHSpermidine synthase 2.5.1.16 0.650