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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
5dx8SFGHistone-arginine methyltransferase CARM1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dx8SFGHistone-arginine methyltransferase CARM1/1.000
5dxaSFGHistone-arginine methyltransferase CARM1/0.683
5dx1SFGHistone-arginine methyltransferase CARM1/0.659
5dxjSFGHistone-arginine methyltransferase CARM1/0.659
3b3fSAHHistone-arginine methyltransferase CARM1/0.649
2y1wSFGHistone-arginine methyltransferase CARM1/0.628
5dwqSFGHistone-arginine methyltransferase CARM1/0.618
2y1xSAHHistone-arginine methyltransferase CARM1/0.614
1f3lSAHProtein arginine N-methyltransferase 3/0.581
4c03SFGProtein arginine N-methyltransferase 6/0.530
2bzgSAHThiopurine S-methyltransferase2.1.1.670.525
5dstSAHProtein arginine N-methyltransferase 82.1.10.522
1p4mADPRiboflavin kinase2.7.1.260.505
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.505
4c04SFGProtein arginine N-methyltransferase 6/0.504
4kwcSAHMethyltransferase domain family/0.504
3up3XCAaceDAF-12/0.502
4m37SAHProtein arginine N-methyltransferase 72.1.10.501
3bgiSAHThiopurine S-methyltransferase2.1.1.670.496
3bgvSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.496
4e2xSAHMethyltransferase/0.495
4qppSAHProtein arginine N-methyltransferase 6/0.495
2a14SAHIndolethylamine N-methyltransferase2.1.1.490.491
3nwb659Catechol O-methyltransferase2.1.1.60.488
3lcvSAM16S rRNA (guanine(1405)-N(7))-methyltransferase2.1.1.1790.486
4necSAHPutative SAM-dependent methyltransferase/0.486
4rv9SAHD-mycarose 3-C-methyltransferase/0.486
1pqc444Oxysterols receptor LXR-beta/0.481
5ekuSAHArginine N-methyltransferase, putative/0.481
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.478
2v74SAHHistone-arginine methyltransferase CARM1/0.477
3up0D7SaceDAF-12/0.477
5je4SAHMethyl transferase/0.477
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.476
5je3SAHMethyl transferase/0.476
4fgzSAHPhosphoethanolamine N-methyltransferase/0.475
1rkhVD2Vitamin D3 receptor/0.474
5envNADAlcohol dehydrogenase 11.1.1.10.474
3t7tSAHUncharacterized protein/0.473
1oriSAHProtein arginine N-methyltransferase 1/0.471
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.471
3qakUKAAdenosine receptor A2a/0.471
1n06ADPRiboflavin kinase2.7.1.260.470
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.470
4ft4SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.468
1gky5GPGuanylate kinase2.7.4.80.467
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.467
2zw9SAMtRNA wybutosine-synthesizing protein 42.1.1.2900.466
4r6xSAHPhosphoethanolamine N-methyltransferase/0.466
5ccxSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.466
2y48FADLysine-specific histone demethylase 1A10.465
4h8004TAldehyde dehydrogenase, dimeric NADP-preferring/0.464
4pneSAHMethyltransferase-like protein/0.464
4ymgSAMPutative SAM-dependent O-methyltranferase/0.464
1rjdSAMLeucine carboxyl methyltransferase 12.1.1.2330.463
2hcdBIVVitamin D3 receptor A/0.463
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.462
1rjeSAHLeucine carboxyl methyltransferase 12.1.1.2330.461
2g8yNADHydroxycarboxylate dehydrogenase B/0.461
2r0pK2CPutative FAD-monooxygenase/0.461
3ou7SAMSAM-dependent methyltransferase/0.461
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.460
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.460
4hy6FJ1Heat shock protein HSP 90-alpha/0.460
4iteTEYVitamin D3 receptor/0.460
1ex75GPGuanylate kinase2.7.4.80.459
1g9rUPFLgtC/0.459
3ou6SAMSAM-dependent methyltransferase/0.459
4ax8SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.459
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.458
2i62SAHNicotinamide N-methyltransferase2.1.1.10.458
3kpjSAHPhenylethanolamine N-methyltransferase2.1.1.280.458
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.458
3qvsNADMyo-inositol-1-phosphate synthase (Ino1)/0.458
3uj7SAMPhosphoethanolamine N-methyltransferase/0.458
1nbiSAMGlycine N-methyltransferase2.1.1.200.457
1x1cSAHC-20 methyltransferase/0.457
2zl9VDAVitamin D3 receptor/0.457
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.457
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.457
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.456
3e8sSAHUncharacterized protein/0.456
3uj8SFGPhosphoethanolamine N-methyltransferase/0.456
1yhjR6CPyridoxal kinase2.7.1.350.455
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3tljSAHUncharacterized protein/0.455
4twnB96Ephrin type-A receptor 32.7.10.10.455
1n08ADPRiboflavin kinase2.7.1.260.454
1skmSAHModification methylase HhaI2.1.1.370.454
4dk70KSOxysterols receptor LXR-beta/0.454
5c1mCLRMu-type opioid receptor/0.454
1p8dCO1Oxysterols receptor LXR-beta/0.453
2zynBCDPeriplasmic binding protein/0.453
3vrwYS5Vitamin D3 receptor/0.453
4rtoSFGDNA adenine methylase2.1.1.720.453
4w6z8IDAlcohol dehydrogenase 11.1.1.10.453
4y1bNAPAntE/0.453
1f5fDHTSex hormone-binding globulin/0.452
1oc1ASVIsopenicillin N synthase1.21.3.10.452
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.452
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.452
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.451
1pw1HELD-alanyl-D-alanine carboxypeptidase3.4.16.40.451
4krhSAMPhosphoethanolamine N-methyltransferase 2/0.451
4xba5GPAprataxin-like protein30.451
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.450
1n4qLYS_CYS_VAL_ILE_LEUGeranylgeranyl transferase type-1 subunit beta2.5.1.590.450
1nhkCMPNucleoside diphosphate kinase2.7.4.60.450
2hb7O1CVitamin D3 receptor/0.450
4u7wNDPMxaA/0.450
5a8eXTKBeta-1 adrenergic receptor/0.450
1reoFADL-amino-acid oxidase1.4.3.20.449
1x1bSAHC-20 methyltransferase/0.449
2iidFADL-amino-acid oxidase1.4.3.20.449
4s1iPLPPyridoxal kinase, putative/0.449
5epeSAHUncharacterized protein/0.449
1mczTDPBenzoylformate decarboxylase4.1.1.70.448
1ve3SAMUncharacterized protein/0.448
2hamC33Vitamin D3 receptor/0.448
2xlsFADPutative flavin-containing monooxygenase/0.448
1af7SAHChemotaxis protein methyltransferase2.1.1.800.447
1jqdSAHHistamine N-methyltransferase2.1.1.80.447
2is0I03Beta-secretase 13.4.23.460.447
4k9nTZDBenzoylformate decarboxylase4.1.1.70.447
5bp9SAHPutative methyltransferase protein/0.447
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.447
1mvtDTMDihydrofolate reductase1.5.1.30.446
1rjgSAHLeucine carboxyl methyltransferase 12.1.1.2330.446
1x1dSAHC-20 methyltransferase/0.446
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.446
2qcuFADAerobic glycerol-3-phosphate dehydrogenase1.1.5.30.446
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
3tm4SAMUncharacterized protein/0.446
4k9oTPPBenzoylformate decarboxylase4.1.1.70.446
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.445
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.445
5icfSAH(S)-norcoclaurine 6-O-methyltransferase/0.445
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.444
1s19MC9Vitamin D3 receptor/0.444
2l0xGDPGTP-binding protein Rheb/0.444
2yg6FADPutrescine oxidase/0.444
2zscBTNTamavidin2/0.444
3tm5SFGUncharacterized protein/0.444
2rh1CAUBeta-2 adrenergic receptor/0.444
1db56INPhospholipase A2, membrane associated/0.443
1knrFADL-aspartate oxidase1.4.3.160.443
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.443
2r8pT6FTransketolase 1/0.443
3afhGSUGlutamate--tRNA ligase 2/0.443
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.443
3o7wSAMLeucine carboxyl methyltransferase 12.1.1.2330.443
4m6l21VDihydrofolate reductase1.5.1.30.443
5ccbSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.443
1qtiGNTAcetylcholinesterase3.1.1.70.442
2xlrFADPutative flavin-containing monooxygenase/0.442
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.442
3friSAH16S rRNA methylase/0.442
3ozsOZSCatechol O-methyltransferase2.1.1.60.442
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.442
3vtdTKDVitamin D3 receptor/0.442
3w0aDS5Vitamin D3 receptor/0.442
3w5tLHPVitamin D3 receptor/0.442
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.442
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.442
4xsrUPGAlr3699 protein/0.442
1lkeDOGBilin-binding protein/0.441
1ot7CHCBile acid receptor/0.441
1s64778Geranylgeranyl transferase type-1 subunit beta2.5.1.590.441
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.441
2harOCCVitamin D3 receptor/0.441
2jb1FADL-amino acid oxidase/0.441
3a783EVVitamin D3 receptor/0.441
3rnoNAPNAD(P)H-hydrate epimerase5.1.99.60.441
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.440
2geuCOKPantothenate kinase2.7.1.330.440
2tplHPPTyrosine phenol-lyase4.1.99.20.440
3axtSAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase/0.440
3sf6FDAGlutaryl-CoA dehydrogenase/0.440
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.440
4pnmNU1Tankyrase-22.4.2.300.440