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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
5dxaSFGHistone-arginine methyltransferase CARM1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dxaSFGHistone-arginine methyltransferase CARM1/1.000
5dx8SFGHistone-arginine methyltransferase CARM1/0.705
3b3fSAHHistone-arginine methyltransferase CARM1/0.645
5dxjSFGHistone-arginine methyltransferase CARM1/0.635
5dx1SFGHistone-arginine methyltransferase CARM1/0.603
2y1wSFGHistone-arginine methyltransferase CARM1/0.599
2y1xSAHHistone-arginine methyltransferase CARM1/0.589
1f3lSAHProtein arginine N-methyltransferase 3/0.585
5dwqSFGHistone-arginine methyltransferase CARM1/0.583
4c03SFGProtein arginine N-methyltransferase 6/0.534
2a14SAHIndolethylamine N-methyltransferase2.1.1.490.532
2bzgSAHThiopurine S-methyltransferase2.1.1.670.518
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.497
3up3XCAaceDAF-12/0.496
4rv9SAHD-mycarose 3-C-methyltransferase/0.494
4kwcSAHMethyltransferase domain family/0.484
5dstSAHProtein arginine N-methyltransferase 82.1.10.484
2i62SAHNicotinamide N-methyltransferase2.1.1.10.478
2kceD16Thymidylate synthase/0.478
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.476
3bgvSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.476
2xlsFADPutative flavin-containing monooxygenase/0.475
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.475
3tljSAHUncharacterized protein/0.475
4ax8SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.475
2hcdBIVVitamin D3 receptor A/0.474
3e8sSAHUncharacterized protein/0.474
3bgiSAHThiopurine S-methyltransferase2.1.1.670.473
3up0D7SaceDAF-12/0.473
4e2xSAHMethyltransferase/0.473
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.472
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.470
1db56INPhospholipase A2, membrane associated/0.469
2x9dITCTetracycline repressor protein class D/0.469
1blzACVIsopenicillin N synthase1.21.3.10.468
1oriSAHProtein arginine N-methyltransferase 1/0.468
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.468
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.467
4krhSAMPhosphoethanolamine N-methyltransferase 2/0.466
1o6qR17Squalene--hopene cyclase4.2.1.1290.465
2v74SAHHistone-arginine methyltransferase CARM1/0.465
3gkiCLRNiemann-Pick C1 protein/0.465
3p9kSAHCaffeic acid O-methyltransferase/0.465
4necSAHPutative SAM-dependent methyltransferase/0.465
1crbRTLRetinol-binding protein 1/0.464
2r8pT6FTransketolase 1/0.464
2zw9SAMtRNA wybutosine-synthesizing protein 42.1.1.2900.464
2zynBCDPeriplasmic binding protein/0.464
3qakUKAAdenosine receptor A2a/0.463
2xveFADPutative flavin-containing monooxygenase/0.462
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
5ekuSAHArginine N-methyltransferase, putative/0.461
5je2SAHMethyl transferase/0.461
1lkeDOGBilin-binding protein/0.460
3nx4NAPPutative oxidoreductase/0.460
4twnB96Ephrin type-A receptor 32.7.10.10.460
5je3SAHMethyl transferase/0.460
1p4mADPRiboflavin kinase2.7.1.260.459
1rjgSAHLeucine carboxyl methyltransferase 12.1.1.2330.459
2hasC3OVitamin D3 receptor/0.459
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.459
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.459
4ia3BIVVitamin D3 receptor A/0.459
4iarERM5-hydroxytryptamine receptor 1B/0.459
4ia1BIVVitamin D3 receptor A/0.458
4u7wNDPMxaA/0.458
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.458
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.457
5je4SAHMethyl transferase/0.457
1drhNAPDihydrofolate reductase1.5.1.30.456
1rjeSAHLeucine carboxyl methyltransferase 12.1.1.2330.455
2ytzSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.455
3c3xNAPEugenol synthase 11.1.1.3180.455
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.455
3q43D66M1 family aminopeptidase3.4.110.455
3sn6P0GBeta-2 adrenergic receptor/0.455
2qcuFADAerobic glycerol-3-phosphate dehydrogenase1.1.5.30.454
2ym1FADPhenylacetone monooxygenase1.14.13.920.454
3nwb659Catechol O-methyltransferase2.1.1.60.454
4fgzSAHPhosphoethanolamine N-methyltransferase/0.454
4m37SAHProtein arginine N-methyltransferase 72.1.10.454
2idkC2FGlycine N-methyltransferase2.1.1.200.453
3gkjHC3Niemann-Pick C1 protein/0.453
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.453
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.453
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.452
5c1mCLRMu-type opioid receptor/0.452
5jtbZMAAdenosine receptor A2a/0.452
3hscADPHeat shock cognate 71 kDa protein/0.451
3vt65YIVitamin D3 receptor/0.451
4ea2RWZDehydrosqualene synthase/0.451
4g95OAGDihydrofolate reductase1.5.1.30.451
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.451
1hfqMOTDihydrofolate reductase1.5.1.30.450
1jr4CL4Catechol O-methyltransferase2.1.1.60.450
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.450
2vqbFADPutative flavin-containing monooxygenase/0.450
3gxoSAHMitomycin biosynthesis 6-O-methyltransferase/0.450
3l0lHC3Nuclear receptor ROR-gamma/0.450
3zecANPAdenosine monophosphate-protein transferase SoFic2.7.7.n10.450
4brdANPEctonucleoside triphosphate diphosphohydrolase I/0.450
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.450
5icfSAH(S)-norcoclaurine 6-O-methyltransferase/0.450
1p8dCO1Oxysterols receptor LXR-beta/0.449
1pq944BOxysterols receptor LXR-beta/0.449
3ou7SAMSAM-dependent methyltransferase/0.449
1x1cSAHC-20 methyltransferase/0.448
2gs9SAHUncharacterized protein/0.448
2r0pK2CPutative FAD-monooxygenase/0.448
4m6l21VDihydrofolate reductase1.5.1.30.448
1rjdSAMLeucine carboxyl methyltransferase 12.1.1.2330.447
1xs7MMIBeta-secretase 13.4.23.460.447
3a783EVVitamin D3 receptor/0.447
3friSAH16S rRNA methylase/0.447
3vc2SAHGeranyl diphosphate 2-C-methyltransferase2.1.1.2550.447
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.447
5ccxSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.447
5dhhDGWNociceptin receptor/0.447
1rk3VDXVitamin D3 receptor/0.446
2fhlBNIAvidin-related protein 4/5/0.446
2in6839Wee1-like protein kinase2.7.10.20.446
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.446
4k9nTZDBenzoylformate decarboxylase4.1.1.70.446
4k9oTPPBenzoylformate decarboxylase4.1.1.70.446
4kvzSAHPtnL protein/0.446
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.446
1v7aFRCAdenosine deaminase3.5.4.40.445
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.445
3dlcSAMSAM (And some other nucleotide) binding motif:Generic methyltransferase/0.445
3inxJZCHeat shock protein HSP 90-alpha/0.445
3kpjSAHPhenylethanolamine N-methyltransferase2.1.1.280.445
4ax8ADPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.445
4dvi2IWTankyrase-12.4.2.300.445
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.445
4i9i1DYTankyrase-12.4.2.300.445
5bp9SAHPutative methyltransferase protein/0.445
5kf8ACOPredicted acetyltransferase/0.445
1f123HCHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1felFENRetinol-binding protein 4/0.444
1p1bSAHGuanidinoacetate N-methyltransferase2.1.1.20.444
3ldgSAHUncharacterized protein/0.444
3tm5SFGUncharacterized protein/0.444
3uj8SFGPhosphoethanolamine N-methyltransferase/0.444
4eiyZMAAdenosine receptor A2a/0.444
4pneSAHMethyltransferase-like protein/0.444
1o6rR19Squalene--hopene cyclase4.2.1.1290.443
1ve3SAMUncharacterized protein/0.443
2bufADPAcetylglutamate kinase/0.443
2hm9TRRDihydrofolate reductase1.5.1.30.443
3uj7SAMPhosphoethanolamine N-methyltransferase/0.443
3vtbTKAVitamin D3 receptor/0.443
4qnvGEKtRNA U34 carboxymethyltransferase/0.443
4ys0ADPProtein translocase subunit SecA/0.443
5irnADPNucleotide binding oligomerization domain containing 2/0.443
1mczTDPBenzoylformate decarboxylase4.1.1.70.442
1nbiSAMGlycine N-methyltransferase2.1.1.200.442
1qtiGNTAcetylcholinesterase3.1.1.70.442
2r0cFADPutative FAD-monooxygenase/0.442
2rbeZMGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3pqbVGPPutative oxidoreductase/0.442
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.442
4r6xSAHPhosphoethanolamine N-methyltransferase/0.442
4ruoBIVVitamin D3 receptor A/0.442
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.442
1h36R88Squalene--hopene cyclase4.2.1.1290.441
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.441
2ed4FAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.441
3exnACOProbable acetyltransferase/0.441
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.441
4trj665Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
4y6nUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.441
5uviZMAAdenosine receptor A2a/0.441
3emlZMAAdenosine receptor A2a/0.441
1g6oADPCag alpha/0.440
1wy7SAHUncharacterized protein/0.440
2fwzH71Heat shock protein HSP 90-alpha/0.440
2lbdREARetinoic acid receptor gamma/0.440
3fyvXCFDihydrofolate reductase1.5.1.30.440
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.440
3wstSAHProtein arginine N-methyltransferase 72.1.10.440
4dh60KNBeta-secretase 13.4.23.460.440
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.440
5kf9ACOPredicted acetyltransferase/0.440
4ug2NGIAdenosine receptor A2a/0.440