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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
2v7uSAM5'-fluoro-5'-deoxy-adenosine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2v7uSAM5'-fluoro-5'-deoxy-adenosine synthase/1.000
2v7tSAH5'-fluoro-5'-deoxy-adenosine synthase/0.806
4araC56Acetylcholinesterase3.1.1.70.519
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.517
1dx6GNTAcetylcholinesterase3.1.1.70.510
3b1dPLSBetaC-S lyase/0.505
3v0p4GWHisto-blood group ABO system transferase/0.502
1pz0NAPProtein IolS1.1.10.496
1votHUPAcetylcholinesterase3.1.1.70.496
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.491
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.491
3fhxPLPPyridoxal kinase2.7.1.350.490
1odcA8BAcetylcholinesterase3.1.1.70.486
1zgbA1EAcetylcholinesterase3.1.1.70.485
2ejzSAHDiphthine synthase/0.481
3r8hZOMAldo-keto reductase family 1 member C3/0.481
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.481
1xdyMTEProtein-methionine-sulfoxide reductase catalytic subunit MsrP/0.480
2ok8FADFerredoxin--NADP reductase, apicoplast/0.478
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.478
1gpnHUBAcetylcholinesterase3.1.1.70.476
3h3r14HCollagen type IV alpha-3-binding protein/0.475
1fx1FMNFlavodoxin/0.474
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.474
1qoqIGPTryptophan synthase alpha chain/0.474
2cekN8TAcetylcholinesterase3.1.1.70.474
2pncCLUPrimary amine oxidase, liver isozyme/0.474
1azlFMNFlavodoxin/0.473
1qtiGNTAcetylcholinesterase3.1.1.70.472
2op18PCEnoyl-ACP reductase/0.471
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.470
2xlpNAPPutative flavin-containing monooxygenase/0.469
4ey7E20Acetylcholinesterase3.1.1.70.469
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.469
1h69ARHNAD(P)H dehydrogenase [quinone] 11.6.5.20.468
4b7zQ4QAcetylcholinesterase3.1.1.70.468
4bfxZVXPantothenate kinase2.7.1.330.468
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
4bfwZVWPantothenate kinase2.7.1.330.467
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.466
2wzySQXSoluble acetylcholine receptor/0.466
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.466
4e32DWNMethyltransferase/0.466
1h22E10Acetylcholinesterase3.1.1.70.465
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.465
1kw8BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.465
1q84TZ4Acetylcholinesterase3.1.1.70.465
2jf0HBPAcetylcholinesterase3.1.1.70.465
4bfvZVVPantothenate kinase2.7.1.330.465
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.465
4du6GTPGTP cyclohydrolase 1/0.465
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.465
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.464
2aj8SC3Dipeptidyl peptidase 4/0.464
2hxzH7JCathepsin S3.4.22.270.464
3pkeY10Methionine aminopeptidase 2/0.464
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.464
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.463
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.463
3juoAJDPhenazine biosynthesis protein A/B/0.463
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.463
3ou6SAMSAM-dependent methyltransferase/0.462
1yw8A75Methionine aminopeptidase 2/0.461
2j3qTFLAcetylcholinesterase3.1.1.70.461
3g0gRUMDipeptidyl peptidase 4/0.461
3vilSA0Beta-glucosidase/0.461
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.461
4m0f1YKAcetylcholinesterase3.1.1.70.461
1b9iPXG3-amino-5-hydroxybenzoate synthase4.2.1.1440.460
4j0p1H8Beta-secretase 13.4.23.460.460
1ahnFMNFlavodoxin 1/0.459
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.459
2ed3SAHDiphthine synthase/0.459
3b9gIMHIAG-nucleoside hydrolase/0.459
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3junAJDPhenazine biosynthesis protein A/B/0.459
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.459
4jxrACOAcetyltransferase/0.458
4x9dU5PUncharacterized protein MJ1435/0.458
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.457
1yhnGTPRas-related protein Rab-7a/0.457
3kmyD8YBeta-secretase 13.4.23.460.457
2c6c24IGlutamate carboxypeptidase 23.4.17.210.456
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.456
3b6pTMPThree-prime repair exonuclease 13.1.11.20.456
3egvSAHRibosomal protein L11 methyltransferase2.1.10.456
1d0lBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.455
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.455
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.455
1ta6177Prothrombin3.4.21.50.455
1u65CP0Acetylcholinesterase3.1.1.70.455
2v9cMREFMN-dependent NADH-azoreductase 1/0.455
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.455
3v0m5GWHisto-blood group ABO system transferase/0.455
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.455
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.454
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.454
3c72CX1Geranylgeranyl transferase type-2 subunit beta2.5.1.600.454
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.454
3qftFADNADPH--cytochrome P450 reductase/0.454
4qenSAHHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH42.1.1.430.454
4tlaADPCircadian clock protein kinase KaiC2.7.11.10.454
4zzjCNANAD-dependent protein deacetylase sirtuin-13.5.10.454
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.453
1h60STRPentaerythritol tetranitrate reductase/0.453
3arvSAUChitinase A/0.453
3hggCHDCmeR/0.453
3nx2FERFerulic acid decarboxylase/0.453
3v0o4GWHisto-blood group ABO system transferase/0.453
3zncBZ1Carbonic anhydrase 44.2.1.10.453
4wxg2BOSerine hydroxymethyltransferase/0.453
1h8hATPATP synthase subunit alpha, mitochondrial/0.452
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.452
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.452
3bm1FMNPutative NAD(P)H nitroreductase YdjA/0.452
4k0tD9ZCarbonic anhydrase 24.2.1.10.452
1m4dCOAAminoglycoside 2'-N-acetyltransferase2.3.10.451
1rsgFADPolyamine oxidase FMS1/0.451
2ew5Y12Peptide deformylase/0.451
2zs8ADPPantothenate kinase2.7.1.330.451
3ie3N11Glutathione S-transferase P2.5.1.180.451
3iu8T03Methionine aminopeptidase 2/0.451
3mauPLRPutative sphingosine-1-phosphate lyase/0.451
4ey6GNTAcetylcholinesterase3.1.1.70.451
5czySAMEukaryotic huntingtin interacting protein B/0.451
1cnfFADNitrate reductase [NADH]1.7.1.10.450
1w4lGL8Acetylcholinesterase3.1.1.70.450
1w76GNTAcetylcholinesterase3.1.1.70.450
3csjCBLGlutathione S-transferase P2.5.1.180.450
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.450
3otwCOAPhosphopantetheine adenylyltransferase/0.450
3pkdY10Methionine aminopeptidase 2/0.450
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.449
1m4iCOAAminoglycoside 2'-N-acetyltransferase2.3.10.449
1w6rGNTAcetylcholinesterase3.1.1.70.449
1yqzCOACoenzyme A disulfide reductase/0.449
2cleF6FTryptophan synthase alpha chain/0.449
2v58LZJBiotin carboxylase6.3.4.140.449
2xupTZ5Acetylcholinesterase3.1.1.70.449
3ai0PNWBeta-glucosidase/0.449
4ap1NAPSteroid monooxygenase/0.449
4arbC57Acetylcholinesterase3.1.1.70.449
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.449
1gt5BZQOdorant-binding protein/0.448
1jdzFMBPurine nucleoside phosphorylase/0.448
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.448
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.448
2jgsBTNAvidin/0.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.448
4azwSAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.448
4bfuZVUPantothenate kinase2.7.1.330.448
4kxjP34Nucleoprotein/0.448
1f20FADNitric oxide synthase, brain1.14.13.390.447
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.447
3d2mCOAAmino-acid acetyltransferase/0.447
3djgFADGlutathione reductase, mitochondrial1.8.1.70.447
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.447
3s2v3HUGlutamate receptor ionotropic, kainate 1/0.447
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.447
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.447
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
4k13ETSCarbonic anhydrase 24.2.1.10.447
1ex75GPGuanylate kinase2.7.4.80.446
1j8qFMNFlavodoxin/0.446
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.446
1tkcM6TTransketolase 12.2.1.10.446
1vgqCAOFormyl-CoA:oxalate CoA-transferase/0.446
1xi2CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.446
3f7bAG5Carbonic anhydrase 44.2.1.10.446
3h3sH15Collagen type IV alpha-3-binding protein/0.446
3pm1ETHTH-type transcriptional regulator QacR/0.446
4ryvZEAProtein LlR18A/0.446
1fmlRTLRetinol dehydratase/0.445
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.445
2a9z26AAdenosine kinase2.7.1.200.445
2w6cBM4Acetylcholinesterase3.1.1.70.445
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.445
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3ewkFADSensory box histidine kinase/response regulator/0.445
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.445
4j7gTRHPCZA361.3/0.445
4uthFMNXenobiotic reductase/0.445
4zvmDM2Ribosyldihydronicotinamide dehydrogenase [quinone]/0.445
1gm9SOXPenicillin G acylase3.5.1.110.444
1i9mINWCarbonic anhydrase 24.2.1.10.444
1sg0STLRibosyldihydronicotinamide dehydrogenase [quinone]/0.444
2aj4ANPGalactokinase2.7.1.60.444
2vqbNAPPutative flavin-containing monooxygenase/0.444
2whqHI6Acetylcholinesterase3.1.1.70.444
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3iexGMPPurine nucleoside phosphorylase/0.444
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.444
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.444
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.444
4j7hTRHPCZA361.3/0.444
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.444
4q7f3D1Uncharacterized protein/0.444
1ay0TPPTransketolase 12.2.1.10.443
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.443
1w4xFADPhenylacetone monooxygenase1.14.13.920.443
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.443
1x1cSAHC-20 methyltransferase/0.443
1xddAAYIntegrin alpha-L/0.443
2aot2PMHistamine N-methyltransferase2.1.1.80.443
2dvoITTdITP/XTP pyrophosphatase3.6.1.190.443
2egbSAHDiphthine synthase/0.443
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.443
2gs9SAHUncharacterized protein/0.443
2npfMOUElongation factor 2/0.443
2ojg19AMitogen-activated protein kinase 12.7.11.240.443
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.443
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.443
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.443
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.443
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.443
4gtp7TPProtein farnesyltransferase subunit beta2.5.1.580.443
4hrqAZGCytidine and deoxycytidylate deaminase zinc-binding region/0.443
4prxADPDNA gyrase subunit B/0.443
1nzq162Prothrombin3.4.21.50.442
1x2eATXProline iminopeptidase3.4.11.50.442
3eksCY9Actin-5C/0.442
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.442
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.442
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.442
3pkbY16Methionine aminopeptidase 2/0.442
3pqbVGPPutative oxidoreductase/0.442
3q43D66M1 family aminopeptidase3.4.110.442
3qgf46FGenome polyprotein2.7.7.480.442
4mhtSAHModification methylase HhaI2.1.1.370.442
1mmkH4BPhenylalanine-4-hydroxylase1.14.16.10.441
1oytFSNProthrombin3.4.21.50.441
1pqc444Oxysterols receptor LXR-beta/0.441
1swgBTNStreptavidin/0.441
1touB1VFatty acid-binding protein, adipocyte/0.441
1ycgFMNNitric oxide reductase10.441
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.441
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2dshSAHDiphthine synthase/0.441
2e07SAHDiphthine synthase/0.441
2gevCOKPantothenate kinase2.7.1.330.441
2ha6SCKAcetylcholinesterase3.1.1.70.441
2pb1NFGGlucan 1,3-beta-glucosidase/0.441
2vbpVB1Isopenicillin N synthase1.21.3.10.441
3b4p3B4Phenazine biosynthesis protein A/B/0.441
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3fp0FP015-O-acetyltransferase/0.441
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.441
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.441
1ascNPLAspartate aminotransferase2.6.1.10.440
1lnmDTXBilin-binding protein/0.440
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.440
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.440
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.440
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1x27ASP_ASP_TYR_VAL_PTRTyrosine-protein kinase Lck2.7.10.20.440
1zhaPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.440
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.440
2gyuHI6Acetylcholinesterase3.1.1.70.440
3dr7GPDGDP-perosamine synthase/0.440
3e78TPPHigh affinity transport system protein p37/0.440
3rviRVIBeta-secretase 13.4.23.460.440
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.440
4b4vL34Bifunctional protein FolD/0.440
4b63NAPL-ornithine N(5)-monooxygenase/0.440
4bftZVTPantothenate kinase2.7.1.330.440
4dymIYZActivin receptor type-12.7.11.300.440
4relKMPGlycosyltransferase/0.440