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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
3kmtSAHHistone H3K27 methylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3kmtSAHHistone H3K27 methylase/1.000
5jhnSAMHistone-lysine N-methyltransferase EHMT2/0.551
5jinSAMHistone-lysine N-methyltransferase EHMT2/0.548
2igqSAHHistone-lysine N-methyltransferase EHMT1/0.523
2o8jSAHHistone-lysine N-methyltransferase EHMT2/0.519
5czySAMEukaryotic huntingtin interacting protein B/0.518
5jj0SAMHistone-lysine N-methyltransferase EHMT2/0.517
3hnaSAHHistone-lysine N-methyltransferase EHMT1/0.516
3fpdSAHHistone-lysine N-methyltransferase EHMT1/0.499
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.498
3ooiSAMHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific2.1.1.430.497
2r3aSAMHistone-lysine N-methyltransferase SUV39H22.1.1.430.496
2g247IGRenin3.4.23.150.490
2iko7IGRenin3.4.23.150.490
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.483
2v13C40Renin3.4.23.150.477
3mj4URMUDP-galactopyranose mutase/0.475
4ypuSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.475
3pdnSFGHistone-lysine N-methyltransferase SMYD32.1.1.430.470
3ru0SFGHistone-lysine N-methyltransferase SMYD32.1.1.430.470
4qenSAHHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH42.1.1.430.468
3hl0NADMaleylacetate reductase/0.465
4o30SAHProbable Histone-lysine N-methyltransferase ATXR52.1.1.430.464
4b7754MBeta-secretase 13.4.23.460.463
3h3qH13Collagen type IV alpha-3-binding protein/0.462
3oqkS52Renin3.4.23.150.462
3h3t16HCollagen type IV alpha-3-binding protein/0.461
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.460
2g1n1IGRenin3.4.23.150.458
3cbpSFGHistone-lysine N-methyltransferase SETD72.1.1.430.458
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.457
2g1o2IGRenin3.4.23.150.457
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1w6hTITPlasmepsin-23.4.23.390.456
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.456
4h12SAHHistone-lysine N-methyltransferase SETD22.1.1.430.456
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.456
1zgbA1EAcetylcholinesterase3.1.1.70.455
2gv8NDPThiol-specific monooxygenase1.14.130.455
2i4qUA4Renin3.4.23.150.455
2rfiSAHHistone-lysine N-methyltransferase EHMT1/0.454
4j83SAMHistone-lysine N-methyltransferase SETD72.1.1.430.453
4ypaSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.453
5irnADPNucleotide binding oligomerization domain containing 2/0.453
4b00I6XBeta-secretase 13.4.23.460.452
4ejvLCLTranscriptional regulator TcaR/0.452
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.452
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.451
4bfzZVZPantothenate kinase2.7.1.330.451
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.450
2j3qTFLAcetylcholinesterase3.1.1.70.450
4oztP1AEcdysone receptor, putative/0.450
4ynpSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.450
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.449
2vn1FK5Peptidylprolyl isomerase/0.449
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.449
4b68NAPL-ornithine N(5)-monooxygenase/0.449
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.448
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.448
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.448
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.448
2g226IGRenin3.4.23.150.448
2xukTZ5Acetylcholinesterase3.1.1.70.448
3oqfS51Renin3.4.23.150.448
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.447
2g21L1BRenin3.4.23.150.447
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
3vyeVYERenin3.4.23.150.447
1icqOPD12-oxophytodienoate reductase 11.3.1.420.446
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.446
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.445
1tsxUMPThymidylate synthase/0.445
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.445
2g1s4IGRenin3.4.23.150.445
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4jt91NSNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.445
2ikuLIYRenin3.4.23.150.444
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.444
3own3OWRenin3.4.23.150.444
1bu5RBFFlavodoxin/0.443
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.443
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2fxuBIDActin, alpha skeletal muscle/0.443
2xupTZ5Acetylcholinesterase3.1.1.70.443
3atzFMNProstaglandin F2a synthase/0.443
3f63GTXGlutathione transferase GST1-4/0.443
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.443
3vucHHERenin3.4.23.150.443
4gdcNDPUDP-galactopyranose mutase/0.443
5f59SAHHistone-lysine N-methyltransferase 2C2.1.1.430.443
2whqHI6Acetylcholinesterase3.1.1.70.442
3ekuCY9Actin-5C/0.442
3v2uATPProtein GAL3/0.442
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
1t2cNAIL-lactate dehydrogenase1.1.1.270.441
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.441
3mauEXTPutative sphingosine-1-phosphate lyase/0.441
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.441
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.441
1q83TZ5Acetylcholinesterase3.1.1.70.440
1x1aSAMC-20 methyltransferase/0.440
2xuoTZ4Acetylcholinesterase3.1.1.70.440
3gqvNAPEnoyl reductase LovC10.440
4e2dFMNDehydrogenase/0.440
4eb7PLPCysteine desulfurase IscS 2/0.440
4m6jNDPDihydrofolate reductase1.5.1.30.440
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.440