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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
3hnaSAHHistone-lysine N-methyltransferase EHMT1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3hnaSAHHistone-lysine N-methyltransferase EHMT1/1.000
3fpdSAHHistone-lysine N-methyltransferase EHMT1/0.617
5jinSAMHistone-lysine N-methyltransferase EHMT2/0.617
2o8jSAHHistone-lysine N-methyltransferase EHMT2/0.601
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.601
5jhnSAMHistone-lysine N-methyltransferase EHMT2/0.599
5jj0SAMHistone-lysine N-methyltransferase EHMT2/0.576
2igqSAHHistone-lysine N-methyltransferase EHMT1/0.573
2rfiSAHHistone-lysine N-methyltransferase EHMT1/0.558
3kmtSAHHistone H3K27 methylase/0.537
5czySAMEukaryotic huntingtin interacting protein B/0.537
3swcSAHHistone-lysine N-methyltransferase EHMT1/0.527
4nv10FXFormyl transferase/0.488
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.487
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.478
4j4nD44Peptidylprolyl isomerase/0.477
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.476
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.476
2xupTZ5Acetylcholinesterase3.1.1.70.473
3ru0SFGHistone-lysine N-methyltransferase SMYD32.1.1.430.472
4j83SAMHistone-lysine N-methyltransferase SETD72.1.1.430.470
3ribSAHN-lysine methyltransferase SMYD2/0.466
1ex75GPGuanylate kinase2.7.4.80.465
3cbpSFGHistone-lysine N-methyltransferase SETD72.1.1.430.465
1q84TZ4Acetylcholinesterase3.1.1.70.464
2iko7IGRenin3.4.23.150.461
4ypaSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.460
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.457
2cekN8TAcetylcholinesterase3.1.1.70.454
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.454
4nv14TGFormyl transferase/0.453
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.452
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.452
2g226IGRenin3.4.23.150.452
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
2ikuLIYRenin3.4.23.150.451
2vn1FK5Peptidylprolyl isomerase/0.451
2g1o2IGRenin3.4.23.150.450
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.450
2eixFADNADH-cytochrome b5 reductase/0.449
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.447
2zgx29UProthrombin3.4.21.50.447
3pdnSFGHistone-lysine N-methyltransferase SMYD32.1.1.430.446
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.445
2ifaFMNUncharacterized protein/0.445
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.445
2zda32UProthrombin3.4.21.50.445
3vqsJT1Genome polyprotein/0.445
4acuQN7Beta-secretase 13.4.23.460.445
1ld8U49Protein farnesyltransferase subunit beta2.5.1.580.444
4djw0KPBeta-secretase 13.4.23.460.444
2wu4HBPAcetylcholinesterase3.1.1.70.443
3mj4URMUDP-galactopyranose mutase/0.443
3tg4SAMN-lysine methyltransferase SMYD2/0.443
4i1c1BEBeta-secretase 13.4.23.460.443
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.442
2dxdANPNucleoside diphosphate kinase2.7.4.60.442
2xukTZ5Acetylcholinesterase3.1.1.70.442
4azy7F3Beta-secretase 13.4.23.460.442
1pqc444Oxysterols receptor LXR-beta/0.441
2ckmAA7Acetylcholinesterase3.1.1.70.441
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.441
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.441
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1cnfFADNitrate reductase [NADH]1.7.1.10.440
2fs4PZ1Renin3.4.23.150.440
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.440
4ypuSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.440