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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
3wv8ATPHmd co-occurring protein HcgE

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3wv8ATPHmd co-occurring protein HcgE/1.000
3wv7ADPHmd co-occurring protein HcgE/0.576
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.510
3c36KAIGlutamate receptor ionotropic, kainate 1/0.505
3uayADNPurine nucleoside phosphorylase DeoD-type/0.495
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.491
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.486
3c34KAIGlutamate receptor ionotropic, kainate 1/0.486
3wqmB29Diterpene synthase3.1.7.80.486
4imfSI3N-acetylneuraminate lyase/0.486
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.485
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.484
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.484
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.482
2po7CHDFerrochelatase, mitochondrial4.99.1.10.479
1lkeDOGBilin-binding protein/0.478
2qs1UB1Glutamate receptor ionotropic, kainate 1/0.477
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.476
2gevCOKPantothenate kinase2.7.1.330.476
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.476
2zevB71Geranylgeranyl pyrophosphate synthase/0.475
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
4b1e6T6Beta-secretase 13.4.23.460.475
2v7qATPATP synthase subunit alpha, mitochondrial/0.473
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.473
2jb2FADL-amino acid oxidase/0.472
2yac937Serine/threonine-protein kinase PLK12.7.11.210.472
4req5ADMethylmalonyl-CoA mutase large subunit5.4.99.20.472
4twnB96Ephrin type-A receptor 32.7.10.10.472
3bi6396Wee1-like protein kinase2.7.10.20.471
4da0GNGPurine nucleoside phosphorylase DeoD-type2.4.2.10.471
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.470
3c35KAIGlutamate receptor ionotropic, kainate 1/0.470
3zkyWT4Isopenicillin N synthase1.21.3.10.470
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
2r0cFADPutative FAD-monooxygenase/0.468
4l7h1W1Beta-secretase 13.4.23.460.468
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.468
1zdfUPGGlycogenin-12.4.1.1860.467
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.467
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.467
4hh4SAHCcbJ/0.467
2flhZEACytokinin-specific binding protein/0.466
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3upr1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.466
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.464
2fjaFADAdenylylsulfate reductase, subunit A (AprA)/0.464
3h1vTK1Glucokinase2.7.1.20.464
4bb3KKAIsopenicillin N synthase1.21.3.10.464
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.464
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.463
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.463
3qakUKAAdenosine receptor A2a/0.463
2j83BATUlilysin3.4.240.462
3af1GDPPantothenate kinase2.7.1.330.462
3ufl508Beta-secretase 13.4.23.460.462
4d79ATPtRNA threonylcarbamoyladenosine dehydratase6.10.462
4o4fATPKinase/0.462
5ccyTMPPolymerase acidic protein/0.462
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3ribSAHN-lysine methyltransferase SMYD2/0.461
4b0532DBeta-secretase 13.4.23.460.461
1aiqCB3Thymidylate synthase/0.460
2az3CDPNucleoside diphosphate kinase/0.460
2pncCLUPrimary amine oxidase, liver isozyme/0.460
3n87N873-dehydroquinate dehydratase4.2.1.100.460
4h3g10QBeta-secretase 13.4.23.460.460
4o4eATPKinase/0.460
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2g2zCOZMalonyl CoA-acyl carrier protein transacylase2.3.1.390.459
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.459
4jx1CAHCamphor 5-monooxygenase1.14.15.10.459
4oztP1AEcdysone receptor, putative/0.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1tv8SAMGTP 3',8-cyclase4.1.99.180.458
2bxtC2DProthrombin3.4.21.50.458
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3fvqATPFe(3+) ions import ATP-binding protein FbpC/0.458
4b7754MBeta-secretase 13.4.23.460.458
3pm1ETHTH-type transcriptional regulator QacR/0.457
3v2uATPProtein GAL3/0.457
1oc1ASVIsopenicillin N synthase1.21.3.10.456
2wjoQUDBeta-secretase 13.4.23.460.456
3up0D7SaceDAF-12/0.456
4fr10V2Queuine tRNA-ribosyltransferase2.4.2.290.456
1e1qANPATP synthase subunit alpha, mitochondrial/0.455
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.455
1e79ATPATP synthase subunit alpha, mitochondrial/0.455
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.455
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.455
1w29TS06,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
2okcSAMProbable type I restriction enzyme BthVORF4518P M protein2.1.1.720.455
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.455
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.455
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
1g63FMNEpidermin decarboxylase4.1.10.454
1t57FMNConserved protein/0.454
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.454
2xytTC9Soluble acetylcholine receptor/0.454
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3up3XCAaceDAF-12/0.454
4h1e10JBeta-secretase 13.4.23.460.454
5fm7ADPRuvB-like helicase/0.454
1mvtDTMDihydrofolate reductase1.5.1.30.453
1pk92FAPurine nucleoside phosphorylase DeoD-type/0.453
2b53D23Cyclin-dependent kinase 22.7.11.220.453
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.453
2iviACWIsopenicillin N synthase1.21.3.10.453
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.453
3v0p4GWHisto-blood group ABO system transferase/0.453
4fm80UQBeta-secretase 13.4.23.460.453
4rdiATPtRNA threonylcarbamoyladenosine dehydratase6.10.453
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.453
1mewXMPInosine-5'-monophosphate dehydrogenase/0.452
1mokFAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.452
1tllFADNitric oxide synthase, brain1.14.13.390.452
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
2hekGDPUncharacterized protein/0.452
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.452
3zoiM2WIsopenicillin N synthase1.21.3.10.452
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.452
4i8vBHFCytochrome P450 1A11.14.14.10.452
4kc1WS1Histo-blood group ABO system transferase/0.452
4zobLGCLin1840 protein/0.452
1kceCB3Thymidylate synthase/0.451
1rfuADPPyridoxal kinase2.7.1.350.451
1u1d181Uridine phosphorylase2.4.2.30.451
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2jb1FADL-amino acid oxidase/0.451
2v16C47Renin3.4.23.150.451
2v57PRLTetR family transcriptional regulator/0.451
2y882ERPhosphoribosyl isomerase A5.3.1.160.451
3br3ETHTH-type transcriptional regulator QacR/0.451
3fktSIIBeta-secretase 13.4.23.460.451
4n3l2FNProthrombin3.4.21.50.451
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.451
1fw0KAIGlutamate receptor 2/0.450
1j9zFADNADPH--cytochrome P450 reductase/0.450
1nm6L86Prothrombin3.4.21.50.450
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.450
3bgxMEFThymidylate synthase/0.450
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3ig6438Urokinase-type plasminogen activator3.4.21.730.450
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.450
4az29MUProthrombin3.4.21.50.450
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1n08ADPRiboflavin kinase2.7.1.260.449
1pq944BOxysterols receptor LXR-beta/0.449
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.449
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.449
3vyeVYERenin3.4.23.150.449
3zxzKRWHepatocyte growth factor receptor2.7.10.10.449
4at0FADPossible succinate dehydrogenase/0.449
4bfyZVYPantothenate kinase2.7.1.330.449
4djx0KQBeta-secretase 13.4.23.460.449
5irnADPNucleotide binding oligomerization domain containing 2/0.449
1g6oADPCag alpha/0.448
1jnzFADAdenylylsulfate reductase, subunit A (AprA)/0.448
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.448
1pfyMSPMethionine--tRNA ligase6.1.1.100.448
1u33LM2Pancreatic alpha-amylase/0.448
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.448
2z4sADPChromosomal replication initiator protein DnaA/0.448
3csoXNIGenome polyprotein2.7.7.480.448
3rsv3RSBeta-secretase 13.4.23.460.448
3v0m5GWHisto-blood group ABO system transferase/0.448
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.448
1rjdSAMLeucine carboxyl methyltransferase 12.1.1.2330.447
2bktRPFRenin3.4.23.150.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3q9bB3NAcetylpolyamine amidohydrolase/0.447
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4fmqANPMitogen-activated protein kinase 12.7.11.240.447
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4gxs0YSGlutamate receptor 2/0.447
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.447
1d9i00PProthrombin3.4.21.50.446
1eveE20Acetylcholinesterase3.1.1.70.446
1gesFADGlutathione reductase1.8.1.70.446
1trgCB3Thymidylate synthase/0.446
1zg32HIIsoflavone 4'-O-methyltransferase/0.446
2fjbSFDAdenylylsulfate reductase, subunit A (AprA)/0.446
2j62GSZO-GlcNAcase NagJ/0.446
2wzySQXSoluble acetylcholine receptor/0.446
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.446
3lpiZ74Beta-secretase 13.4.23.460.446
3v0o4GWHisto-blood group ABO system transferase/0.446
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.446
4ho4THMGlucose-1-phosphate thymidylyltransferase/0.446
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
2isc223Purine nucleoside phosphorylase, putative/0.445
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.445
2zz0FADThioredoxin reductase 1, cytoplasmic1.8.1.90.445
3b7dCNIGlutamate receptor 2/0.445
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.445
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.445
3h0bB35Beta-secretase 13.4.23.460.445
4awmKDHPolymerase acidic protein/0.445
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.445
2cleF6FTryptophan synthase alpha chain/0.444
2ejzSAHDiphthine synthase/0.444
2pj4414Carboxypeptidase B/0.444
2y1wSFGHistone-arginine methyltransferase CARM1/0.444
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.444
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.444
4bis8HQLysine-specific demethylase 4A1.14.110.444
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.444
4h5cYS4Farnesyl pyrophosphate synthase2.5.1.100.444
4jx1CAMCamphor 5-monooxygenase1.14.15.10.444
4xba5GPAprataxin-like protein30.444
5dp2NAPCurF/0.444
5f8eSAHPossible transcriptional regulatory protein/0.444
5fl3ADPPili retraction protein PilT/0.444
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
1ndzFR5Adenosine deaminase3.5.4.40.443
1pd9CO4Dihydrofolate reductase1.5.1.30.443
1zgaHMKIsoflavone 4'-O-methyltransferase/0.443
2bsxNOSPurine nucleoside phosphorylase/0.443
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.443
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.443
4az3S35Lysosomal protective protein3.4.16.50.443
4bdoKAIGlutamate receptor ionotropic, kainate 2/0.443
4bfzZVZPantothenate kinase2.7.1.330.443
4foxUMPThymidylate synthase ThyA/0.443
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.443
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.443
4q15HFGProline--tRNA ligase6.1.1.150.443
4yekTHMThymidine phosphorylase/0.443
5je3SAHMethyl transferase/0.443
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.442
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.442
2g263LGRenin3.4.23.150.442
2vczVC3Hematopoietic prostaglandin D synthase/0.442
2w6cBM4Acetylcholinesterase3.1.1.70.442
3adaNADSubunit alpha of sarocosine oxidase/0.442
3g70A5TRenin3.4.23.150.442
3le62BZCyclin-dependent kinase 22.7.11.220.442
4ba5PXGProbable aminotransferase/0.442
4bfsZVSPantothenate kinase2.7.1.330.442
4ube2FAAdenosine kinase2.7.1.200.442
1b2lNDCAlcohol dehydrogenase1.1.1.10.441
1ml6GBXGlutathione S-transferase A22.5.1.180.441
1mrqSTRAldo-keto reductase family 1 member C1/0.441
1pg0MODMethionine--tRNA ligase6.1.1.100.441
1t4v14AProthrombin3.4.21.50.441
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2cduFADNADH oxidase/0.441
2clmF6FTryptophan synthase alpha chain/0.441
2d1tSLULuciferin 4-monooxygenase1.13.12.70.441
2e07SAHDiphthine synthase/0.441
2wo7ASVIsopenicillin N synthase1.21.3.10.441
2zsdCOAPantothenate kinase2.7.1.330.441
3h2sNDPPutative NADH-flavin reductase/0.441
3h3sH15Collagen type IV alpha-3-binding protein/0.441
3lthUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
3qwiCUE17beta-hydroxysteroid dehydrogenase/0.441
3uwlFOZThymidylate synthase/0.441
4askK0ILysine-specific demethylase 6B1.14.110.441
4h3i10VBeta-secretase 13.4.23.460.441
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.441
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.441
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1obnASVIsopenicillin N synthase1.21.3.10.440
2dshSAHDiphthine synthase/0.440
2fs4PZ1Renin3.4.23.150.440
2lfoGCHFatty acid-binding protein, liver/0.440
2xveFADPutative flavin-containing monooxygenase/0.440
3dejRXCCaspase-33.4.22.560.440
3fowIMHPurine nucleoside phosphorylase/0.440
3kxw1ZZSaframycin Mx1 synthetase B/0.440
3qgf46FGenome polyprotein2.7.7.480.440
3rupADPBiotin carboxylase6.3.4.140.440
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.440
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.440
4nv14TGFormyl transferase/0.440
5i39FADL-amino acid deaminase/0.440