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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
3rq6APRADP-dependent (S)-NAD(P)H-hydrate dehydratase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3rq6APRADP-dependent (S)-NAD(P)H-hydrate dehydratase/1.000
3rqhB6PADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.641
3rqqBA3ADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.616
3rq8AP5ADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.603
1rneC60Renin3.4.23.150.494
2g1r3IGRenin3.4.23.150.491
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.490
2i4qUA4Renin3.4.23.150.487
3oqkS52Renin3.4.23.150.486
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.483
1gqtACPRibokinase/0.482
2ikuLIYRenin3.4.23.150.480
1xddAAYIntegrin alpha-L/0.479
1bil0IURenin3.4.23.150.478
1orrNADCDP-paratose 2-epimerase/0.477
1t88CAMCamphor 5-monooxygenase1.14.15.10.476
3oibFDAPutative acyl-CoA dehydrogenase/0.476
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.474
2iko7IGRenin3.4.23.150.474
5dp2NAPCurF/0.473
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.472
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.472
1f8fNADBenzyl alcohol dehydrogenase/0.471
2y3rTRKTamL/0.471
4g7gVFVLanosterol 14-alpha-demethylase/0.471
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.470
2dcnADP2-keto-3-deoxy-gluconate kinase/0.470
3gfbNADL-threonine 3-dehydrogenase/0.470
3gw9VNILanosterol 14-alpha-demethylase/0.470
3oqfS51Renin3.4.23.150.470
3umoATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.470
5a3bAPRSIR2 family protein/0.470
3gbuATPUncharacterized sugar kinase PH14592.7.10.469
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.469
1fy7COAHistone acetyltransferase ESA1/0.467
3uylTYDProbable NDP-rhamnosyltransferase/0.467
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.466
2givACOHistone acetyltransferase KAT8/0.466
2po7CHDFerrochelatase, mitochondrial4.99.1.10.466
2q5g1FAPeroxisome proliferator-activated receptor delta/0.466
3nsh957Beta-secretase 13.4.23.460.466
4i0i957Beta-secretase 13.4.23.460.466
1mjbACOHistone acetyltransferase ESA1/0.464
3vyeVYERenin3.4.23.150.464
4uyf73BBromodomain-containing protein 2/0.463
1cjkFOKAdenylate cyclase type 2/0.462
1cjkFOKAdenylate cyclase type 5/0.462
1g63FMNEpidermin decarboxylase4.1.10.462
1jioDEB6-deoxyerythronolide B hydroxylase/0.462
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.462
2g1s4IGRenin3.4.23.150.462
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.462
3hyoADPPyridoxal kinase/0.462
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.462
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.461
3c15FOKAdenylate cyclase type 2/0.461
3c15FOKAdenylate cyclase type 5/0.461
3uqdATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.461
5jscFADPutative acyl-CoA dehydrogenase/0.461
1fxsNAPGDP-L-fucose synthase/0.460
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1lbcCYZGlutamate receptor 2/0.460
2c29NAPDihydroflavonol 4-reductase/0.460
2iqgF2IBeta-secretase 13.4.23.460.460
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.460
1adfTADAlcohol dehydrogenase E chain1.1.1.10.459
1me6IVSPlasmepsin-23.4.23.390.459
2g5cNADPrephenate dehydrogenase/0.459
2il2LIXRenin3.4.23.150.459
2xhd7T9Glutamate receptor 2/0.459
4e2bFMNDehydrogenase/0.459
4jjiNADAlcohol dehydrogenase class-3/0.459
4jlm1NNDeoxycytidine kinase2.7.1.740.459
1fm4DXCMajor pollen allergen Bet v 1-L/0.458
1ipeNDPTropinone reductase 21.1.1.2360.458
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.458
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.458
1mj9COAHistone acetyltransferase ESA1/0.458
1tehNADAlcohol dehydrogenase class-31.1.1.10.458
2ahrNAPPyrroline-5-carboxylate reductase/0.458
2fzwNADAlcohol dehydrogenase class-31.1.1.10.458
2q4bNAPUncharacterized protein At5g02240/0.458
3b70NAPEnoyl reductase LovC10.458
3fwjCAMCamphor 5-monooxygenase1.14.15.10.458
3own3OWRenin3.4.23.150.458
4q71FADBifunctional protein PutA/0.458
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.457
1yb5NAPQuinone oxidoreductase1.6.5.50.457
2ed3SAHDiphthine synthase/0.457
2ejvNADL-threonine 3-dehydrogenase/0.457
4kbyC2EStimulator of interferon genes protein/0.457
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1y9dTPPPyruvate oxidase1.2.3.30.456
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3lqfNADGalactitol dehydrogenase/0.456
1bwsNDPGDP-L-fucose synthase/0.455
1phgMYTCamphor 5-monooxygenase1.14.15.10.455
1xe55FEPlasmepsin-23.4.23.390.455
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.455
2bgiFADNADPH:ferredoxin reductase/0.455
3vvpBNUUncharacterized protein/0.455
4e5yNDPGDP-L-fucose synthase1.1.1.2710.455
2qo9ANPEphrin type-A receptor 32.7.10.10.454
2viyVG3Beta-secretase 13.4.23.460.454
2xpuTDCTetracycline repressor protein class D/0.454
3ieuGDPGTPase Era/0.454
3mjhGTPRas-related protein Rab-5A/0.454
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.454
4emtC2EStimulator of interferon genes protein/0.454
1mjaCOAHistone acetyltransferase ESA1/0.453
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.453
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
2g247IGRenin3.4.23.150.453
2ifaFMNUncharacterized protein/0.453
3cid318Beta-secretase 13.4.23.460.453
3crzFADFerredoxin--NADP+ reductase/0.453
3fwgCAMCamphor 5-monooxygenase1.14.15.10.453
3ohh3HHBeta-secretase 13.4.23.460.453
3toxNAPPutative oxidoreductase/0.453
4bfvZVVPantothenate kinase2.7.1.330.453
1cjvFOKAdenylate cyclase type 2/0.452
1cjvFOKAdenylate cyclase type 5/0.452
2y0mACOHistone acetyltransferase KAT8/0.452
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.452
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
4m4922YL-lactate dehydrogenase A chain1.1.1.270.452
1culFOKAdenylate cyclase type 2/0.451
1culFOKAdenylate cyclase type 5/0.451
1g6kNADGlucose 1-dehydrogenase1.1.1.470.451
1i5cADPChemotaxis protein CheA2.7.13.30.451
1y0s331Peroxisome proliferator-activated receptor delta/0.451
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.451
2vkeTACTetracycline repressor protein class D/0.451
2y05NAPProstaglandin reductase 1/0.451
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.451
3iaeD7KBenzaldehyde lyase/0.451
3vydVYDRenin3.4.23.150.451
3wfjNAD2-dehydropantoate 2-reductase/0.451
4jbqVX6Aurora kinase A2.7.11.10.451
4jx1CAHCamphor 5-monooxygenase1.14.15.10.451
4tuvCPZCytochrome P450 1191.140.451
4u0mGTPCyclic GMP-AMP synthase/0.451
4zs2FLUAlpha-ketoglutarate-dependent dioxygenase FTO/0.451
1drhNAPDihydrofolate reductase1.5.1.30.450
1e3eNAIAlcohol dehydrogenase 41.1.1.10.450
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
3qwbNDPProbable quinone oxidoreductase1.6.5.50.450
3sdkP3NProteasome subunit beta type-53.4.25.10.450
3sdkP3NProteasome subunit beta type-63.4.25.10.450
3slkNDPPolyketide synthase extender module 2/0.450
3vucHHERenin3.4.23.150.450
4dbzNDPPutative ketoacyl reductase1.3.10.450
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.450
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.450
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1x8lOXRRetinol dehydratase/0.449
2aa0MTPAdenosine kinase2.7.1.200.449
2xaaNADSecondary alcohol dehydrogenase/0.449
3ai3NDPNADPH-sorbose reductase/0.449
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3l63CAMCamphor 5-monooxygenase1.14.15.10.449
3lpiZ74Beta-secretase 13.4.23.460.449
3sf6FDAGlutaryl-CoA dehydrogenase/0.449
4aosFADSteroid monooxygenase/0.449
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.449
4g3jVNTLanosterol 14-alpha-demethylase/0.449
4uymVOR14-alpha sterol demethylase Cyp51B/0.449
1g1aNADdTDP-glucose 4,6-dehydratase/0.448
1rv1IMZE3 ubiquitin-protein ligase Mdm26.3.20.448
1w5tANPORC1-type DNA replication protein 2/0.448
2du8FADD-amino-acid oxidase1.4.3.30.448
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.448
2g20L1ARenin3.4.23.150.448
3d2pCOAAmino-acid acetyltransferase/0.448
3uqdADPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.448
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.448
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.448
2e16SAHDiphthine synthase/0.447
2y3sTIRTamL/0.447
3cukFADD-amino-acid oxidase1.4.3.30.447
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.447
3d91REMRenin3.4.23.150.447
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.447
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.447
4kqwNAPKetol-acid reductoisomerase (NADP(+))/0.447
4loqSB4Mitogen-activated protein kinase 14/0.447
4wjiNAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase/0.447
1ppjANYCytochrome b/0.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.446
2f1kNAPPrephenate dehydrogenase/0.446
2ou2ACOHistone acetyltransferase KAT5/0.446
2v16C47Renin3.4.23.150.446
2vcmM11Isopenicillin N synthase1.21.3.10.446
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.446
2yxuATPPyridoxal kinase2.7.1.350.446
3cic316Beta-secretase 13.4.23.460.446
3dm6757Beta-secretase 13.4.23.460.446
3qofGDPAtlastin-13.6.50.446
3r96ACOMccE protein/0.446
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.446
3vswR31Renin3.4.23.150.446
4b1rITCTetracycline repressor protein class D/0.446
4bfxZVXPantothenate kinase2.7.1.330.446
4dt9GMPAPH(2'')-Id/0.446
4j7uNAPSepiapterin reductase1.1.1.1530.446
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.446
4zohFADPutative oxidoreductase FAD-binding subunit/0.446
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.445
1ia1NDPDihydrofolate reductase1.5.1.30.445
2gjlFMNNitronate monooxygenase1.13.12.160.445
2rcyNAPPyrroline-5-carboxylate reductase/0.445
2xx91NFGlutamate receptor 2/0.445
3c1y2BADNA integrity scanning protein DisA/0.445
3f3sNADLambda-crystallin homolog/0.445
3fwiCAMCamphor 5-monooxygenase1.14.15.10.445
4fg8ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.445
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.444
2wo7ASVIsopenicillin N synthase1.21.3.10.444
2y3rTIRTamL/0.444
3dmeFADPutative conserved exported protein/0.444
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.444
3veu0GOBeta-secretase 13.4.23.460.444
3vqsJT1Genome polyprotein/0.444
4hjfC2EGGDEF family protein/0.444
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.444
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1t2cNAIL-lactate dehydrogenase1.1.1.270.443
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.443
1w6hTITPlasmepsin-23.4.23.390.443
1y4lSVRBasic phospholipase A2 homolog 2/0.443
2a94AP0L-lactate dehydrogenase1.1.1.270.443
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.443
2iyaZIOOleandomycin glycosyltransferase/0.443
2xtnGTPGTPase IMAP family member 2/0.443
3d8bADPFidgetin-like protein 13.6.40.443
3ixj586Beta-secretase 13.4.23.460.443
3vyfVYFRenin3.4.23.150.443
4n9iPCGCatabolite expression activator/0.443
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.443
4xguADPPutative pachytene checkpoint protein 2/0.443
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.443
1cf3FADGlucose oxidase1.1.3.40.442
2bu9HFVIsopenicillin N synthase1.21.3.10.442
2owuSAHDiphthine synthase/0.442
2vnjFADNADPH:ferredoxin reductase/0.442
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
3clsFADElectron transfer flavoprotein subunit alpha/0.442
3d7kD7KBenzaldehyde lyase/0.442
3ih0ANPUncharacterized sugar kinase PH14592.7.10.442
3in6FMNUncharacterized protein/0.442
3lpjZ75Beta-secretase 13.4.23.460.442
3sdi3SDProteasome subunit beta type-53.4.25.10.442
3sdi3SDProteasome subunit beta type-63.4.25.10.442
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.442
4r81FMNPredicted NADH dehydrogenase/0.442
4xr9NADCalS8/0.442
5a3cNADSIR2 family protein/0.442
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.442
5fl3ADPPili retraction protein PilT/0.442
5hxwFADL-amino acid deaminase/0.442
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.441
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.441
1pq944BOxysterols receptor LXR-beta/0.441
1qrpHH0Pepsin A-43.4.23.10.441
1xuoLA1Integrin alpha-L/0.441
2g1y5IGRenin3.4.23.150.441
2wf4ZY4Beta-secretase 13.4.23.460.441
2ylzFADPhenylacetone monooxygenase1.14.13.920.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3mdmFJZCholesterol 24-hydroxylase/0.441
3vmmP0DAlanine--anticapsin ligase/0.441
3zuyTCHTransporter/0.441
4dplNAPMalonyl-CoA reductase1.2.1.750.441
4ejvLCLTranscriptional regulator TcaR/0.441
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.441
4frkDWDBeta-secretase 13.4.23.460.441
4jazSTLPeroxisome proliferator-activated receptor gamma/0.441
1bsvNDPGDP-L-fucose synthase/0.440
1kkq471Peroxisome proliferator-activated receptor alpha/0.440
1mp0NADAlcohol dehydrogenase class-31.1.1.10.440
2b8l5HABeta-secretase 13.4.23.460.440
2ev9NAPShikimate dehydrogenase (NADP(+))/0.440
2p6kSAHDiphthine synthase/0.440
2zb3NDPProstaglandin reductase 21.3.1.480.440
2zuiCAMCamphor 5-monooxygenase1.14.15.10.440
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.440
3ctyFADProbable thioredoxin reductase/0.440
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
3ik6HCZGlutamate receptor 2/0.440
3ivcFG4Pantothenate synthetase6.3.2.10.440
3lpkZ76Beta-secretase 13.4.23.460.440
4b3aTACTetracycline repressor protein class D/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4enhFVXCholesterol 24-hydroxylase/0.440
4gl4NAIAlcohol dehydrogenase class-3/0.440
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.440
4qzuRTLRetinol-binding protein 2/0.440
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.440
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.440