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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2onyTMJPhenylethanolamine N-methyltransferase2.1.1.28

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2onyTMJPhenylethanolamine N-methyltransferase2.1.1.281.000
2onzTMJPhenylethanolamine N-methyltransferase2.1.1.280.770
2opbF21Phenylethanolamine N-methyltransferase2.1.1.280.761
2obfF83Phenylethanolamine N-methyltransferase2.1.1.280.651
2g8nF83Phenylethanolamine N-methyltransferase2.1.1.280.603
2g72F21Phenylethanolamine N-methyltransferase2.1.1.280.562
3dlcSAMSAM (And some other nucleotide) binding motif:Generic methyltransferase/0.494
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.489
1gj5130Prothrombin3.4.21.50.481
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.481
2bf7HBIPteridine reductase 11.5.1.330.477
3hnzPMN3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.477
1b3dS27Stromelysin-13.4.24.170.476
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.475
4zu44TGWxcM-like protein/0.475
1lcwSHMStreptavidin/0.474
1qzzSAMAclacinomycin 10-hydroxylase RdmB4.1.10.474
3mp5HMGHydroxymethylglutaryl-CoA lyase, mitochondrial4.1.3.40.474
2hveADPNucleoside diphosphate kinase A2.7.4.60.473
3ix4TX1Transcriptional activator protein LasR/0.473
3h3t16HCollagen type IV alpha-3-binding protein/0.472
1o2g696Prothrombin3.4.21.50.470
3i53SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase/0.470
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.469
1jtuLYBThymidylate synthase/0.468
1nhkCMPNucleoside diphosphate kinase2.7.4.60.468
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.468
1c4uIH1Prothrombin3.4.21.50.467
1g49111Stromelysin-13.4.24.170.467
3v0p4GWHisto-blood group ABO system transferase/0.467
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.466
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.466
2bfmTOPPteridine reductase 11.5.1.330.465
1re0AFBADP-ribosylation factor 1/0.463
1re0AFBARF guanine-nucleotide exchange factor 1/0.463
4hr2ADPNucleoside diphosphate kinase/0.463
2xi4AFTAcetylcholinesterase3.1.1.70.462
3h3qH13Collagen type IV alpha-3-binding protein/0.462
4ixc1JDGlucokinase2.7.1.20.462
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.461
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.460
3vf60H6Glucokinase2.7.1.20.460
4jpg1OXPyruvate kinase PKM2.7.1.400.459
4twnB96Ephrin type-A receptor 32.7.10.10.459
1d8mBBHStromelysin-13.4.24.170.458
2z2dHSIMacrophage metalloelastase3.4.24.650.458
3h3r14HCollagen type IV alpha-3-binding protein/0.458
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.458
2v57PRLTetR family transcriptional regulator/0.457
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.457
3geyP34Poly [ADP-ribose] polymerase 152.4.2.300.457
4nmcFADBifunctional protein PutA/0.457
1biwS80Stromelysin-13.4.24.170.456
1w6jR71Lanosterol synthase5.4.99.70.456
3ohoZ79Stromelysin-13.4.24.170.456
1dgfNDPCatalase1.11.1.60.454
1o5gCR9Prothrombin3.4.21.50.454
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.454
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
3w5uFADFerredoxin/0.453
4l091URTankyrase-22.4.2.300.453
4mzuTYDWxcM-like protein/0.453
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.452
2watCOAFatty acid synthase subunit alpha2.3.1.860.452
3sfh1DIHistone deacetylase 83.5.1.980.452
3wnzADPAlanine--anticapsin ligase/0.452
2ea2F77Methionine aminopeptidase 2/0.451
2ji7ADPOxalyl-CoA decarboxylase4.1.1.80.451
4zdcCO83,2-trans-enoyl-CoA isomerase5.3.3.80.451
3iexGMPPurine nucleoside phosphorylase/0.450
1jf0CZHObelin/0.449
2cn0F25Prothrombin3.4.21.50.449
3h4vDVPPteridine reductase 11.5.1.330.449
3ivcFG4Pantothenate synthetase6.3.2.10.449
3ix8TX3Transcriptional activator protein LasR/0.449
4araC56Acetylcholinesterase3.1.1.70.449
4ggzBTNBll1558 protein/0.449
1be4PCGNucleoside diphosphate kinase A 22.7.4.60.448
1uhhCZPAequorin-2/0.448
3lm4HPXCatechol 2,3-dioxygenase/0.448
3v0o4GWHisto-blood group ABO system transferase/0.448
4dz5NAPAldo-keto reductase family 1 member C3/0.448
4n4v2GYTankyrase-12.4.2.300.448
1amoFADNADPH--cytochrome P450 reductase/0.447
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.447
2hvdADPNucleoside diphosphate kinase A2.7.4.60.447
2jibADPOxalyl-CoA decarboxylase4.1.1.80.447
2w6cBM4Acetylcholinesterase3.1.1.70.447
3gy9COAGCN5-related N-acetyltransferase/0.447
3ipuO40Oxysterols receptor LXR-alpha/0.447
4a6nT1CTetX family tetracycline inactivation enzyme/0.447
4dvi2IWTankyrase-12.4.2.300.447
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.447
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2aclL05Oxysterols receptor LXR-alpha/0.446
2d1oFA4Stromelysin-13.4.24.170.446
3c34KAIGlutamate receptor ionotropic, kainate 1/0.446
3s41S41Glucokinase2.7.1.20.446
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.446
4ea2RWZDehydrosqualene synthase/0.446
4nqgCZHMitrocomin/0.446
1nceCB3Thymidylate synthase/0.445
1xr2C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.445
2cf9348Prothrombin3.4.21.50.445
2ji9ADPOxalyl-CoA decarboxylase4.1.1.80.445
2tscCB3Thymidylate synthase/0.445
2yhuWHFPteridine reductase/0.445
3arvSAUChitinase A/0.445
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.444
1bqoN25Stromelysin-13.4.24.170.444
1cq6PY4Aspartate aminotransferase2.6.1.10.444
1nueGDPNucleoside diphosphate kinase B2.7.4.60.444
1sazACPProbable butyrate kinase 2/0.444
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.444
1s7gNADNAD-dependent protein deacylase 2/0.443
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.443
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.443
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.443
2az3CDPNucleoside diphosphate kinase/0.443
2hk9NAPShikimate dehydrogenase (NADP(+))/0.443
2jddACOProbable acetyltransferase/0.443
2ytzSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.443
4g67SAHUncharacterized ACR, COG1565 superfamily/0.443
4kc1WS1Histo-blood group ABO system transferase/0.443
4wx2F6FTryptophan synthase alpha chain/0.443
4wx2F6FTryptophan synthase beta chain4.2.1.200.443
1d9i00PProthrombin3.4.21.50.442
2wjoQUDBeta-secretase 13.4.23.460.442
2zevB71Geranylgeranyl pyrophosphate synthase/0.442
3pkbY16Methionine aminopeptidase 2/0.442
3tfyMET_LEU_GLY_PRON-alpha-acetyltransferase 502.3.10.442
3x1dGDPAtlastin3.6.50.442
4n1fCZHObelin/0.442
4o8jADNRNA 3'-terminal phosphate cyclase6.5.1.40.442
4xbjIN5Alanine racemase, biosynthetic/0.442
1sjwNGVNogalonic acid methyl ester cyclase/0.441
2dxfGNPNucleoside diphosphate kinase2.7.4.60.441
2zymACXPeriplasmic binding protein/0.441
3iktNADRedox-sensing transcriptional repressor Rex/0.441
3qwc98PProthrombin3.4.21.50.441
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.441
4ynpSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.441
2rh1CAUBeta-2 adrenergic receptor/0.441
4gbrCAUBeta-2 adrenergic receptor/0.441
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.440
2a4xBLMMitomycin-binding protein/0.440
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.440
3pg3DG7Mitogen-activated protein kinase 14/0.440
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.440
4dpeNGHStromelysin-13.4.24.170.440
4iwv1J9Glucokinase2.7.1.20.440
4l8u9AZSerum albumin/0.440