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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
1f3lSAHProtein arginine N-methyltransferase 3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1f3lSAHProtein arginine N-methyltransferase 3/1.000
2y1wSFGHistone-arginine methyltransferase CARM1/0.593
2y1xSAHHistone-arginine methyltransferase CARM1/0.575
5dwqSFGHistone-arginine methyltransferase CARM1/0.574
5dx1SFGHistone-arginine methyltransferase CARM1/0.565
5dx8SFGHistone-arginine methyltransferase CARM1/0.563
5dxjSFGHistone-arginine methyltransferase CARM1/0.556
5dxaSFGHistone-arginine methyltransferase CARM1/0.554
3b3fSAHHistone-arginine methyltransferase CARM1/0.548
4c03SFGProtein arginine N-methyltransferase 6/0.532
4rv9SAHD-mycarose 3-C-methyltransferase/0.499
3bgiSAHThiopurine S-methyltransferase2.1.1.670.494
2bzgSAHThiopurine S-methyltransferase2.1.1.670.493
1x1cSAHC-20 methyltransferase/0.490
4ax8SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.478
1nbiSAMGlycine N-methyltransferase2.1.1.200.475
4ft4SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.473
5icfSAH(S)-norcoclaurine 6-O-methyltransferase/0.473
3tm5SFGUncharacterized protein/0.471
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.471
3dlcSAMSAM (And some other nucleotide) binding motif:Generic methyltransferase/0.467
1x1bSAHC-20 methyltransferase/0.465
3tm4SAMUncharacterized protein/0.463
4kwcSAHMethyltransferase domain family/0.463
3p9kSAHCaffeic acid O-methyltransferase/0.462
3oqkS52Renin3.4.23.150.461
1rjgSAHLeucine carboxyl methyltransferase 12.1.1.2330.457
3o7wSAMLeucine carboxyl methyltransferase 12.1.1.2330.456
2hizLIJBeta-secretase 13.4.23.460.454
3tljSAHUncharacterized protein/0.454
4c04SFGProtein arginine N-methyltransferase 6/0.454
5envNADAlcohol dehydrogenase 11.1.1.10.454
1oriSAHProtein arginine N-methyltransferase 1/0.452
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.452
1p8dCO1Oxysterols receptor LXR-beta/0.451
3gxoSAHMitomycin biosynthesis 6-O-methyltransferase/0.451
4r6xSAHPhosphoethanolamine N-methyltransferase/0.450
3ldgSAHUncharacterized protein/0.449
1xs7MMIBeta-secretase 13.4.23.460.448
3ou6SAMSAM-dependent methyltransferase/0.447
5dstSAHProtein arginine N-methyltransferase 82.1.10.447
1rjdSAMLeucine carboxyl methyltransferase 12.1.1.2330.446
3fktSIIBeta-secretase 13.4.23.460.446
3q9bB3NAcetylpolyamine amidohydrolase/0.446
4b66NAPL-ornithine N(5)-monooxygenase/0.445
3skgPB8Beta-secretase 13.4.23.460.444
5f8eSAHPossible transcriptional regulatory protein/0.444
3ou7SAMSAM-dependent methyltransferase/0.443
3t7tSAHUncharacterized protein/0.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.442
3cic316Beta-secretase 13.4.23.460.442
4kvzSAHPtnL protein/0.442
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.441
3cid318Beta-secretase 13.4.23.460.441
3dv1AR9Beta-secretase 13.4.23.460.441
4e2xSAHMethyltransferase/0.441
3dv5BAVBeta-secretase 13.4.23.460.440
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.440
4ymgSAMPutative SAM-dependent O-methyltranferase/0.440