Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4gc9SAMDimethyladenosine transferase 1, mitochondrial2.1.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4gc9SAMDimethyladenosine transferase 1, mitochondrial2.1.11.000
1qanSAHrRNA adenine N-6-methyltransferase2.1.1.1840.526
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.520
2yr5FADPhenylalanine 2-monooxygenase precursor1.13.12.90.507
1ve3SAMUncharacterized protein/0.501
3grrSAHProbable ribosomal RNA small subunit methyltransferase A/0.501
3ha5SFGHydroxymycolate synthase MmaA42.1.10.501
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.495
3uj8SFGPhosphoethanolamine N-methyltransferase/0.495
4qnuGEKtRNA U34 carboxymethyltransferase/0.489
1qaoSAMrRNA adenine N-6-methyltransferase2.1.1.1840.488
1qaqSFGrRNA adenine N-6-methyltransferase2.1.1.1840.488
3s1sSAHRestriction endonuclease BpuSI/0.488
2w06FRVCyclin-dependent kinase 22.7.11.220.487
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.486
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.486
3oibFDAPutative acyl-CoA dehydrogenase/0.484
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.484
3tm5SFGUncharacterized protein/0.483
2ylsFADPhenylacetone monooxygenase1.14.13.920.482
2ylzFADPhenylacetone monooxygenase1.14.13.920.482
5epeSAHUncharacterized protein/0.481
1n4uFAECholesterol oxidase1.1.3.60.480
3orhSAHGuanidinoacetate N-methyltransferase2.1.1.20.480
2wa2SAMGenome polyprotein/0.479
4y9qC2EUncharacterized protein/0.478
5br7FADUDP-galactopyranose mutase/0.478
2ylrNAPPhenylacetone monooxygenase1.14.13.920.477
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.477
2qe6SAMUncharacterized protein/0.476
4v2gITCTetracycline repressor protein class D/0.476
1f0xFADD-lactate dehydrogenase1.1.1.280.475
4wa9AXITyrosine-protein kinase ABL12.7.10.20.475
3tm4SAMUncharacterized protein/0.473
1likADNAdenosine kinase2.7.1.200.472
2h3wCOACarnitine O-acetyltransferase2.3.1.70.472
4iv0SAMPhosphoethanolamine N-methyltransferase, putative/0.471
4mihFADPyranose 2-oxidase1.1.3.100.471
2ad5ADPCTP synthase/0.468
2pxaSAHGenome polyprotein2.7.7.480.468
2vkeTACTetracycline repressor protein class D/0.467
2ylxFADPhenylacetone monooxygenase1.14.13.920.467
3gyiFADCholesterol oxidase1.1.3.60.467
4u2lSFDCholesterol oxidase1.1.3.60.467
5idwNAPShort-chain dehydrogenase/reductase SDR/0.467
2i62SAHNicotinamide N-methyltransferase2.1.1.10.466
2vprTDCTetracycline repressor protein class H/0.466
3o6o94MHeat shock protein 83/0.465
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.465
4mwzSAMPhosphoethanolamine N-methyltransferase, putative/0.465
1mxtFAECholesterol oxidase1.1.3.60.464
3gw9VNILanosterol 14-alpha-demethylase/0.464
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.464
3vwdACOAlpha-tubulin N-acetyltransferase 1/0.464
2xpvMIYTetracycline repressor protein class D/0.463
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.463
3i0pNADMalate dehydrogenase, putative/0.463
3sr4TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.463
4rekFADCholesterol oxidase1.1.3.60.463
5bp7SAHSAM-dependent methyltransferase/0.463
3d8bADPFidgetin-like protein 13.6.40.462
3friSAH16S rRNA methylase/0.462
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.462
3tljSAHUncharacterized protein/0.462
5a3bAPRSIR2 family protein/0.462
1h7wFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.461
2rcyNAPPyrroline-5-carboxylate reductase/0.461
3ha3SAHHydroxymycolate synthase MmaA42.1.10.461
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.461
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.461
4g67SAHUncharacterized ACR, COG1565 superfamily/0.461
4wq5ATPtRNA N6-adenosine threonylcarbamoyltransferase/0.461
2ym2FADPhenylacetone monooxygenase1.14.13.920.460
3go4SAHUncharacterized protein/0.460
3p9kSAHCaffeic acid O-methyltransferase/0.460
4d03NAPPhenylacetone monooxygenase1.14.13.920.460
4oknNAIL-lactate dehydrogenase A chain1.1.1.270.460
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.460
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.459
2cduFADNADH oxidase/0.459
2gs9SAHUncharacterized protein/0.459
4ambDUDPutative glycosyl transferase/0.459
4pd6URINucleoside permease/0.459
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.458
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.458
3gqvNAPEnoyl reductase LovC10.458
4a2bAGSCell division protein FtsA/0.458
4g6hNAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.458
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.457
2fk8SAMHydroxymycolate synthase MmaA42.1.10.457
2fznFADBifunctional protein PutA1.5.5.20.457
4b1bFADThioredoxin reductase1.8.1.90.457
1jioDEB6-deoxyerythronolide B hydroxylase/0.456
2zb3NDPProstaglandin reductase 21.3.1.480.456
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.456
3nxxNDPDihydrofolate reductase1.5.1.30.456
4awq592Heat shock protein HSP 90-alpha/0.456
4jldADPAdenylate kinase/0.456
4xxgFADCholesterol oxidase1.1.3.60.456
1eqyATPActin, alpha skeletal muscle/0.455
1nbiSAMGlycine N-methyltransferase2.1.1.200.455
2bi4NADLactaldehyde reductase1.1.1.770.455
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.455
3ix8TX3Transcriptional activator protein LasR/0.455
3p8zSAHGenome polyprotein2.1.1.560.455
4a2aATPCell division protein FtsA/0.455
4dwvNAJAlcohol dehydrogenase E chain1.1.1.10.455
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.455
1me6IVSPlasmepsin-23.4.23.390.454
2bl4NADLactaldehyde reductase1.1.1.770.454
3h0sB38Acetyl-CoA carboxylase/0.454
3sz0FADSulfide-quinone reductase/0.454
5dp2NAPCurF/0.454
1ot7IU5Bile acid receptor/0.453
1p0hACOMycothiol acetyltransferase2.3.1.1890.453
1w2xRCPAcetyl-CoA carboxylase/0.453
2fiwACOGCN5-related N-acetyltransferase:Aminotransferase, class-II/0.453
2pwySAHtRNA (adenine(58)-N(1))-methyltransferase TrmI2.1.1.2200.453
2y0mACOHistone acetyltransferase KAT8/0.453
3b70NAPEnoyl reductase LovC10.453
3oqfS51Renin3.4.23.150.453
4b7754MBeta-secretase 13.4.23.460.453
3sn6P0GBeta-2 adrenergic receptor/0.453
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.452
1ppjANYCytochrome b/0.452
1sg9SAMRelease factor glutamine methyltransferase2.1.1.2970.452
1tj0FADBifunctional protein PutA1.5.5.20.452
2trtTACTetracycline repressor protein class D/0.452
2xrlDXTTetracycline repressor protein class D/0.452
2zevB71Geranylgeranyl pyrophosphate synthase/0.452
4c0bATPmRNA cleavage and polyadenylation factor CLP1/0.452
4er6AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.452
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.452
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1s22ATPActin, alpha skeletal muscle/0.451
2fy4COACholine O-acetyltransferase2.3.1.60.451
3hazFADBifunctional protein PutA/0.451
3kpkFADSulfide-quinone reductase/0.451
3p8z36AGenome polyprotein2.1.1.560.451
3qlsNDPDihydrofolate reductase1.5.1.30.451
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.451
4qi5FADCellobiose dehydrogenase/0.451
5bp9SAHPutative methyltransferase protein/0.451
5dbgNADIridoid synthase1.3.1.990.451
5je2SAHMethyl transferase/0.451
1b8sFADCholesterol oxidase1.1.3.60.450
1g67TZPThiamine-phosphate synthase/0.450
2ebaFADPutative glutaryl-CoA dehydrogenase/0.450
4d03FADPhenylacetone monooxygenase1.14.13.920.450
4oplFDAConserved Archaeal protein/0.450
3p0gP0GBeta-2 adrenergic receptor/0.450
1ia1NDPDihydrofolate reductase1.5.1.30.449
1psa0ZLPepsin A3.4.23.10.449
1pz0NAPProtein IolS1.1.10.449
2iko7IGRenin3.4.23.150.449
3deiRXBCaspase-33.4.22.560.449
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.449
4pyoSAHCatechol O-methyltransferase2.1.1.60.449
4xwrFADCholesterol oxidase1.1.3.60.449
1xe55FEPlasmepsin-23.4.23.390.448
2g20L1ARenin3.4.23.150.448
2gciMRRProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.448
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.448
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.448
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.448
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.448
3e2sFADBifunctional protein PutA1.5.5.20.448
3evcSAHGenome polyprotein2.1.1.560.448
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.448
3slkNDPPolyketide synthase extender module 2/0.448
4z26FADPutative GMC-type oxidoreductase R13510.448
1h2bNAJNAD-dependent alcohol dehydrogenase/0.447
1uhjCZBAequorin-2/0.447
2npaMMBPeroxisome proliferator-activated receptor alpha/0.447
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.447
3gbuATPUncharacterized sugar kinase PH14592.7.10.447
3jzdNADMaleylacetate reductase/0.447
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.447
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.447
4necSAHPutative SAM-dependent methyltransferase/0.447
4wxxSAHDNA (cytosine-5)-methyltransferase 12.1.1.370.447
5envNADAlcohol dehydrogenase 11.1.1.10.447
5ez7FADProbable FAD-dependent oxidoreductase PA4991/0.447
1ai9NDPDihydrofolate reductase1.5.1.30.446
1okkGCPSignal recognition particle protein/0.446
1okkGCPSignal recognition particle receptor FtsY/0.446
1s7gAPRNAD-dependent protein deacylase 2/0.446
2d4vNADIsocitrate dehydrogenase [NADP]/0.446
2f8lSAMLmo1582 protein/0.446
3gyjFADCholesterol oxidase1.1.3.60.446
3q87SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY)/0.446
3tfyCOAN-alpha-acetyltransferase 502.3.10.446
3ujlA8SAbscisic acid receptor PYL2/0.446
4c49HCYCorticosteroid-binding globulin/0.446
4ci6ATPActin/0.446
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.446
4kfn1QRNicotinamide phosphoribosyltransferase2.4.2.120.446
4q71FADBifunctional protein PutA/0.446
4ryvZEAProtein LlR18A/0.446
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.446
5lc1NADL-threonine 3-dehydrogenase/0.446
1drhNAPDihydrofolate reductase1.5.1.30.445
1osvCHCBile acid receptor/0.445
1pjkANPCasein kinase II subunit alpha2.7.11.10.445
1tj1FADBifunctional protein PutA1.5.5.20.445
1xddAAYIntegrin alpha-L/0.445
2p41SAHGenome polyprotein/0.445
3k4nFADPyranose 2-oxidase/0.445
4ctkSAMGenome polyprotein/0.445
1lf3EH5Plasmepsin-23.4.23.390.444
1pqc444Oxysterols receptor LXR-beta/0.444
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.444
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.444
1rx1NAPDihydrofolate reductase1.5.1.30.444
1uyePU9Heat shock protein HSP 90-alpha/0.444
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.444
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.444
2xpuTDCTetracycline repressor protein class D/0.444
2ym1NAPPhenylacetone monooxygenase1.14.13.920.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.444
4jx1CAHCamphor 5-monooxygenase1.14.15.10.444
4k43ADPActin, alpha skeletal muscle/0.444
4kl9NDPDihydrofolate reductase1.5.1.30.444
4tlbAGSCircadian clock protein kinase KaiC2.7.11.10.444
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.443
1hzzNAPNAD(P) transhydrogenase subunit beta1.6.1.20.443
1meiXMPInosine-5'-monophosphate dehydrogenase/0.443
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.443
2dteNAIGlucose 1-dehydrogenase related protein/0.443
2w2lNADD-mandelate dehydrogenase/0.443
3oht1N1Mitogen-activated protein kinase/0.443
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.443
4xq9NADHomospermidine synthase2.5.1.440.443
4xrgNADHomospermidine synthase2.5.1.440.443
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.442
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.442
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.442
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
2gd6ACOProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.442
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.442
3aw9NADNAD-dependent epimerase/dehydratase/0.442
3cnjFADCholesterol oxidase1.1.3.60.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.442
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.442
4j6bPLOCytochrome P450 monooxygenase/0.442
4o281QSNicotinamide phosphoribosyltransferase2.4.2.120.442
4p2lFADSulfhydryl oxidase 11.8.3.20.442
4w6z8IDAlcohol dehydrogenase 11.1.1.10.442
4z24FADPutative GMC-type oxidoreductase R13510.442
5cmsAPRO-acetyl-ADP-ribose deacetylase/0.442
4ldlXQCBeta-2 adrenergic receptor/0.442
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.441
1qo8FADFumarate reductase flavoprotein subunit/0.441
2b03TUDPhospholipase A2, major isoenzyme3.1.1.40.441
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.441
2nyuSAMrRNA methyltransferase 2, mitochondrial/0.441
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
2ylrFADPhenylacetone monooxygenase1.14.13.920.441
3hyoADPPyridoxal kinase/0.441
3hz5Z64Heat shock protein HSP 90-alpha/0.441
3in6FMNUncharacterized protein/0.441
3is9AC7Gag-Pol polyprotein2.7.7.490.441
4ejmNAPPutative zinc-binding dehydrogenase/0.441
4jlj1NMDeoxycytidine kinase2.7.1.740.441
4k6mSAHGenome polyprotein/0.441
4yntFDAGlucose oxidase, putative/0.441
5bw4SAMUncharacterized protein/0.441
1hncGDNGlutathione S-transferase Mu 22.5.1.180.440
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.440
1zdwFLVPrenyltransferase/0.440
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.440
2prbCOAAminoglycoside 6-N-acetyltransferase type Ib11/0.440
2q7vFADThioredoxin reductase/0.440
2xvfFADPutative flavin-containing monooxygenase/0.440
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.440
3dr8ACOL-methionine sulfoximine/L-methionine sulfone acetyltransferase/0.440
3jpuTY4Transcriptional activator protein LasR/0.440
3ssoSAHMycinamicin VI 2''-O-methyltransferase/0.440
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.440
4dpwAGSMevalonate diphosphate decarboxylase/0.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4l9q9TPSerum albumin/0.440