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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
3elu SAM Methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3elu SAMMethyltransferase / 0.813
2p41 SAHGenome polyprotein / 0.772
3p97 SAMGenome polyprotein 2.1.1.56 0.772
2px5 SAHGenome polyprotein 2.7.7.48 0.768
3eva SAHGenome polyprotein 2.1.1.56 0.766
3p8z SAHGenome polyprotein 2.1.1.56 0.766
3evc SAHGenome polyprotein 2.1.1.56 0.765
3eld SFGMethyltransferase / 0.764
3evb SAHGenome polyprotein 2.1.1.56 0.759
4ctk SAMGenome polyprotein / 0.759
4k6m SAHGenome polyprotein / 0.757
3emd SFGMethyltransferase / 0.755
3ely SAHMethyltransferase / 0.753
2px2 SAHGenome polyprotein 2.7.7.48 0.750
3lkz SFGGenome polyprotein / 0.749
5jjr SAHGenome polyprotein / 0.747
1r6a SAHGenome polyprotein 2.7.7.48 0.745
4ctj SAMGenome polyprotein / 0.745
1wrl TFPTroponin C, slow skeletal and cardiac muscles / 0.744
1xrp PRO_LEU_GLY_GLYProline iminopeptidase 3.4.11.5 0.744
3gww SFXNa(+):neurotransmitter symporter (Snf family) / 0.744
3qa2 XNAKetohexokinase / 0.744
2pxa SAHGenome polyprotein 2.7.7.48 0.741
3p8z 36AGenome polyprotein 2.1.1.56 0.738
1l9k SAHGenome polyprotein 2.7.7.48 0.729
5jjs SAHGenome polyprotein / 0.720
5dto SAHGenome polyprotein / 0.717
2wa2 SAMGenome polyprotein / 0.714
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.710
1o6q R17Squalene--hopene cyclase 4.2.1.129 0.709
2c7x NRBCytochrome P450 monooxygenase PikC / 0.709
3gwu SRENa(+):neurotransmitter symporter (Snf family) / 0.709
3p8h P8HLethal(3)malignant brain tumor-like protein 1 / 0.709
3u9n 09HSerine/threonine-protein kinase Chk1 2.7.11.1 0.709
4a5y G7XKinesin-like protein KIF11 / 0.709
4b76 PW1Genome polyprotein 3.4.21.98 0.709
4iyg 1HUStrictosidine synthase 4.3.3.2 0.709
5dhh DGWNociceptin receptor / 0.709
3pbl ETQD(3) dopamine receptor / 0.709
2p3q SAHGenome polyprotein / 0.698
3evg SAHGenome polyprotein 2.1.1.56 0.698
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.687
2p1d SAHGenome polyprotein 2.7.7.48 0.685
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.685
1w6j R71Lanosterol synthase 5.4.99.7 0.682
2hz4 4STTyrosine-protein kinase ABL1 2.7.10.2 0.682
2q72 IXXNa(+):neurotransmitter symporter (Snf family) / 0.682
2qei CXXNa(+):neurotransmitter symporter (Snf family) / 0.682
3lw0 CCXInsulin-like growth factor 1 receptor 2.7.10.1 0.682
3q92 XNBKetohexokinase / 0.682
3tos SAHCalS11 / 0.682
4i1r LZUMucosa-associated lymphoid tissue lymphoma translocation protein 1 3.4.22 0.682
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.682
4ej4 EJ4Delta-type opioid receptor / 0.682
2xbm SAHGenome polyprotein / 0.681
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.680
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.677
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.676
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.671
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.670
3c3y SAHO-methyltransferase / 0.669
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.668
1zzq DP9Nitric oxide synthase, brain 1.14.13.39 0.666
1zzr DP9Nitric oxide synthase, brain 1.14.13.39 0.666
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.666
2wog ZZDKinesin-like protein KIF11 / 0.666
3cxw 7CPSerine/threonine-protein kinase pim-1 2.7.11.1 0.666
3ken ZZDKinesin-like protein KIF11 / 0.666
3uix Q17Serine/threonine-protein kinase pim-1 2.7.11.1 0.666
4a51 DQ8Kinesin-like protein KIF11 / 0.666
4lm5 Q17Serine/threonine-protein kinase pim-1 2.7.11.1 0.666
4mmd 29ENa(+):neurotransmitter symporter (Snf family) / 0.666
4y4j LNREndothiapepsin 3.4.23.22 0.666
1nw5 SAMModification methylase RsrI 2.1.1.72 0.665
2opb F21Phenylethanolamine N-methyltransferase 2.1.1.28 0.664
2qju DSMNa(+):neurotransmitter symporter (Snf family) / 0.660
2yne YNEGlycylpeptide N-tetradecanoyltransferase / 0.660
3psu LJGGag-Pol polyprotein 3.4.23.16 0.660
3v1s 0LHStrictosidine synthase 4.3.3.2 0.660
4fgj 1PQRibosyldihydronicotinamide dehydrogenase [quinone] / 0.660
4xp4 COCSodium-dependent dopamine transporter / 0.660
5dhg DGVNociceptin receptor / 0.660
2g1p SAHDNA adenine methylase 2.1.1.72 0.659
1yf3 SAHDNA adenine methylase / 0.658
4l9i 8PRRhodopsin kinase / 0.657
2yxl SFG450aa long hypothetical fmu protein / 0.655
1sn5 T3Transthyretin / 0.653
4ea1 3RXDehydrosqualene synthase / 0.653
4mxa BK7Calmodulin-like domain protein kinase isoenzyme gamma, related / 0.653
1q0r AKTAclacinomycin methylesterase RdmC 3.1.1.95 0.652
1q0z AKAAclacinomycin methylesterase RdmC 3.1.1.95 0.652
2c6h PXICytochrome P450 monooxygenase PikC / 0.652
2cd8 PXICytochrome P450 monooxygenase PikC / 0.652
2pjl 047Steroid hormone receptor ERR1 / 0.652
2vzm NRBCytochrome P450 monooxygenase PikC / 0.652
3ko0 TFPProtein S100-A4 / 0.652
3m0w P77Protein S100-A4 / 0.652
4mm4 8PRNa(+):neurotransmitter symporter (Snf family) / 0.652
4uck SAMLarge structural protein / 0.652
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.652
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.652
1skm SAHModification methylase HhaI 2.1.1.37 0.650