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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
3fd6ADPSelenide, water dikinase 12.7.9.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3fd6ADPSelenide, water dikinase 12.7.9.31.000
3c9sACPThiamine-monophosphate kinase/0.516
3c9rATPThiamine-monophosphate kinase/0.514
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.504
4anwO92Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.499
2vesGVRUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.498
3mdvCL6Cholesterol 24-hydroxylase/0.498
3tm5SFGUncharacterized protein/0.495
2lbaCHOFatty acid binding protein 6/0.494
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.494
1yvj4STTyrosine-protein kinase JAK32.7.10.20.492
2qo9ANPEphrin type-A receptor 32.7.10.10.490
2yyeAPCSelenide, water dikinase2.7.9.30.490
4b2gV1NUncharacterized protein/0.490
3s1dZIRCytokinin dehydrogenase 11.5.99.120.486
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.484
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.480
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.478
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.477
1nzdUPGDNA beta-glucosyltransferase/0.475
3lqfNADGalactitol dehydrogenase/0.474
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
2ejvNADL-threonine 3-dehydrogenase/0.472
3h06VBPGlutamate receptor 2/0.472
4a99FADTetX family tetracycline inactivation enzyme/0.472
4bbe3O4Tyrosine-protein kinase JAK2/0.472
5hwsNAP2-dehydropantoate 2-reductase/0.472
1cjtFOKAdenylate cyclase type 2/0.471
1cjtFOKAdenylate cyclase type 5/0.471
1jgtAPCCarboxyethyl-arginine beta-lactam-synthase6.3.3.40.471
1xjjDGTVitamin B12-dependent ribonucleotide reductase/0.471
2yxuATPPyridoxal kinase2.7.1.350.471
4a8v2ANMajor pollen allergen Bet v 1-J/0.471
3keuATPPyridoxal kinase2.7.1.350.470
5fkoTDCTetracycline repressor protein class D/0.470
2henADPEphrin type-B receptor 22.7.10.10.469
3dd125DGlycogen phosphorylase, liver form2.4.1.10.469
4dbzNDPPutative ketoacyl reductase1.3.10.469
4hvi19STyrosine-protein kinase JAK32.7.10.20.469
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.467
2xpvMIYTetracycline repressor protein class D/0.467
3aezGDPPantothenate kinase2.7.1.330.467
3u9eCOALmo1369 protein/0.467
4cukNAID-lactate dehydrogenase/0.467
4dpuAGSMevalonate diphosphate decarboxylase/0.467
4en4ATPPyridoxal kinase2.7.1.350.467
3ibqATPPyridoxal kinase/0.466
3qaiXNNKetohexokinase/0.466
4a6nFADTetX family tetracycline inactivation enzyme/0.466
4k33ACPFibroblast growth factor receptor 32.7.10.10.466
2zsaADPPantothenate kinase2.7.1.330.465
3gdvTYR_GLN_PHESerine endoprotease DegS3.4.21.1070.465
2rioADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.464
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.464
3kbz2T4Fructose-1,6-bisphosphatase 13.1.3.110.464
1nzfUPGDNA beta-glucosyltransferase/0.463
2zs9ADPPantothenate kinase2.7.1.330.463
1bx6BA1cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
3gfbNADL-threonine 3-dehydrogenase/0.462
4dymIYZActivin receptor type-12.7.11.300.462
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.462
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.462
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.461
2qllPLPGlycogen phosphorylase, liver form2.4.1.10.461
3a1nNADNDP-sugar epimerase/0.461
3e8xNAPBH1520 protein/0.461
4dc0NDPPutative ketoacyl reductase1.3.10.461
1culFOKAdenylate cyclase type 2/0.460
1culFOKAdenylate cyclase type 5/0.460
1ptjSNDNAD(P) transhydrogenase subunit alpha part 11.6.1.20.460
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.460
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.460
3umoATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.460
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.460
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.460
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.460
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.459
1jpaANPEphrin type-B receptor 22.7.10.10.458
1q3aNGHStromelysin-23.4.24.220.458
1u54ACPActivated CDC42 kinase 1/0.458
2qoqANPEphrin type-A receptor 32.7.10.10.458
3gwfFADCyclohexanone monooxygenase/0.458
4jqlVJ6Heat shock protein HSP 90-alpha/0.458
4lch1WNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.458
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.457
4eiqKCTPutative FAD-monooxygenase/0.457
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.457
1aj8COACitrate synthase/0.456
1l8qADPChromosomal replication initiator protein DnaA/0.456
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.456
3zdnFADMonoamine oxidase N1.4.3.40.456
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4l0qNADAlcohol dehydrogenase class-3/0.456
4m2bUPGUDP-glucose pyrophosphorylase/0.456
4oaeCLMUncharacterized protein/0.456
1i59ANPChemotaxis protein CheA2.7.13.30.455
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
3fpjSAMUncharacterized protein/0.455
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.455
3phiNDPShikimate dehydrogenase (NADP(+))/0.455
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.455
4gxs0YSGlutamate receptor 2/0.455
4ivgANPTNF receptor-associated protein 1/0.455
4otpADPSerine/threonine-protein kinase RIO12.7.11.10.455
1e8hADPVanillyl-alcohol oxidase1.1.3.380.454
1u28NADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.454
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.454
3nwzCOABH2602 protein/0.454
3oom507Activin receptor type-12.7.11.300.454
3otwCOAPhosphopantetheine adenylyltransferase/0.454
4dpy2P0Mevalonate diphosphate decarboxylase/0.454
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.454
4enhFVXCholesterol 24-hydroxylase/0.454
5hpyGDPTransforming protein RhoA/0.454
1qiqACCIsopenicillin N synthase1.21.3.10.453
2py3ACPFibroblast growth factor receptor 2/0.453
2v7a627Tyrosine-protein kinase ABL12.7.10.20.453
2xw19NVSerum albumin/0.453
3af0GDPPantothenate kinase2.7.1.330.453
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.453
3il1B5DGlutamate receptor 2/0.453
3k5uPFQAurora kinase A2.7.11.10.453
3w1tWRODihydroorotate dehydrogenase (fumarate)1.3.98.10.453
4bgg844Activin receptor type-12.7.11.300.453
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.452
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.452
2an9GDPGuanylate kinase2.7.4.80.452
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.452
2d8aNADL-threonine 3-dehydrogenase/0.452
3b9lAZZSerum albumin/0.452
3bkbSTUTyrosine-protein kinase Fes/Fps2.7.10.20.452
3ddw055Glycogen phosphorylase, liver form2.4.1.10.452
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.452
3q92XNBKetohexokinase/0.452
3repATPIntegrin-linked protein kinase2.7.11.10.452
4g3jVNTLanosterol 14-alpha-demethylase/0.452
4q71FADBifunctional protein PutA/0.452
4yxm2BADNA integrity scanning protein DisA/0.452
5cvhADPCasein kinase II subunit alpha2.7.11.10.452
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.451
1j1bANPGlycogen synthase kinase-3 beta2.7.11.260.451
2cy0NAPShikimate dehydrogenase (NADP(+))/0.451
2xpuTDCTetracycline repressor protein class D/0.451
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.451
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.451
3qiyQI1Botulinum neurotoxin type A3.4.24.690.451
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.451
4gk2L66Ephrin type-A receptor 32.7.10.10.451
5f54TMPSingle-stranded-DNA-specific exonuclease/0.451
1ha3MAUElongation factor Tu-A/0.450
1i5bANPChemotaxis protein CheA2.7.13.30.450
1rfvADPPyridoxal kinase2.7.1.350.450
2e9dB76Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.450
2pvhP19Casein kinase II subunit alpha2.7.11.10.450
3fhyATPPyridoxal kinase2.7.1.350.450
3nbvANPKetohexokinase/0.450
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.450
4dn5AGSMitogen-activated protein kinase kinase kinase 142.7.11.250.450
4eerFMNPhototropin-22.7.11.10.450
4gvjADPNon-receptor tyrosine-protein kinase TYK22.7.10.20.450
4nmdFDABifunctional protein PutA/0.450
1p9wANPType II secretion system protein E/0.449
2jfgUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.449
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.449
2xvv9DNSerum albumin/0.449
3hy9098A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.449
3imgBZ2Pantothenate synthetase6.3.2.10.449
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.449
1llzFMNFerredoxin-dependent glutamate synthase 21.4.7.10.448
1orkATCTetracycline repressor protein class D/0.448
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.448
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
2y3rTRKTamL/0.448
3c1y2BADNA integrity scanning protein DisA/0.448
3dds26BGlycogen phosphorylase, liver form2.4.1.10.448
3f46I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.448
3r9iADPSeptum site-determining protein MinD/0.448
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.448
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1i5aACPChemotaxis protein CheA2.7.13.30.447
1nytNAPShikimate dehydrogenase (NADP(+))/0.447
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.447
2zpaADPtRNA(Met) cytidine acetyltransferase TmcA/0.447
3dagFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.447
3gduTYR_ARG_PHESerine endoprotease DegS3.4.21.1070.447
4fg9ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.447
4gmy0X5Tyrosine-protein kinase JAK2/0.447
4h3ySAHtRNA (guanine-N(1)-)-methyltransferase/0.447
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.447
5fkmTDCTetracycline repressor protein class D/0.447
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.446
1ex75GPGuanylate kinase2.7.4.80.446
1hk1T44Serum albumin/0.446
1kqwRTLCellular retinol-binding protein type II/0.446
2ft9CHDFatty acid-binding protein 2, liver/0.446
2o7pNAPRiboflavin biosynthesis protein RibD/0.446
3c212BADNA integrity scanning protein DisA/0.446
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3mdmFJZCholesterol 24-hydroxylase/0.446
4bibIEOMitogen-activated protein kinase kinase kinase 52.7.11.250.446
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.446
4jazSTLPeroxisome proliferator-activated receptor gamma/0.446
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
1bwlFMNNADPH dehydrogenase 11.6.99.10.445
1ffuFADCarbon monoxide dehydrogenase medium chain/0.445
1fm4DXCMajor pollen allergen Bet v 1-L/0.445
1j39UPGDNA beta-glucosyltransferase/0.445
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.445
2a8h4NHDisintegrin and metalloproteinase domain-containing protein 173.4.24.860.445
2acxANPG protein-coupled receptor kinase 62.7.11.160.445
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.445
2trtTACTetracycline repressor protein class D/0.445
3ad9FADSubunit beta of sarcosine oxidase/0.445
3cehAVEGlycogen phosphorylase, liver form2.4.1.10.445
3clrFADElectron transfer flavoprotein subunit alpha/0.445
3cy2MB9Serine/threonine-protein kinase pim-12.7.11.10.445
3uyt0CKCasein kinase I isoform delta2.7.11.10.445
3zc6VFCTyrosine-protein kinase JAK32.7.10.20.445
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.445
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.445
1uadGNPRas-related protein Ral-A/0.444
1ypkCCRProthrombin3.4.21.50.444
2q46NAPUncharacterized protein At5g02240/0.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3nwq2NCGag-Pol polyprotein3.4.23.160.444
3p2oNADBifunctional protein FolD/0.444
3t2sAGSHeat shock protein HSP 90-alpha/0.444
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.444
4ctaATPCinA-like protein/0.444
4g7gVFVLanosterol 14-alpha-demethylase/0.444
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.444
5dstSAHProtein arginine N-methyltransferase 82.1.10.444
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.443
1xddAAYIntegrin alpha-L/0.443
2gblATPCircadian clock protein kinase KaiC2.7.11.10.443
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.443
2oapANPType II secretion system protein (GspE-2)/0.443
2uzfCAA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.443
2vd0D27Hematopoietic prostaglandin D synthase/0.443
2zbaZBATrichothecene 3-O-acetyltransferase/0.443
3ft8MOJHeat shock protein HSP 90-alpha/0.443
3mtfA3FActivin receptor type-12.7.11.300.443
3nl6TPSUncharacterized protein/0.443
4egbNADdTDP-glucose 4,6-dehydratase/0.443
4ki8ADP60 kDa chaperonin/0.443
4zohFADPutative oxidoreductase FAD-binding subunit/0.443
1bwsNDPGDP-L-fucose synthase/0.442
1f8fNADBenzyl alcohol dehydrogenase/0.442
2bw7ECSAdenylate cyclase/0.442
2ehuNAD1-pyrroline-5-carboxylate dehydrogenase/0.442
2fsvNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.442
2h8hH8HProto-oncogene tyrosine-protein kinase Src2.7.10.20.442
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.442
2o7oDXTTetracycline repressor protein class D/0.442
2pd7FADVivid PAS protein VVD/0.442
3cgdCOACoenzyme A disulfide reductase/0.442
3nxe2NCProtease/0.442
3poz03PEpidermal growth factor receptor2.7.10.10.442
3pp1IZGDual specificity mitogen-activated protein kinase kinase 12.7.12.20.442
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
4a84DXCMajor pollen allergen Bet v 1-A/0.442
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4e4m0NHTyrosine-protein kinase JAK2/0.442
4eh9IRGMitogen-activated protein kinase 14/0.442
4h3zSAHtRNA (guanine-N(1)-)-methyltransferase/0.442
4hvg19QTyrosine-protein kinase JAK32.7.10.20.442
4oauADP2-5A-dependent ribonuclease3.1.260.442
5e8wSTUTGF-beta receptor type-12.7.11.300.442
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kt6RTLRetinol-binding protein 4/0.441
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.441
2npnSAMPutative cobalamin synthesis related protein/0.441
2qc8ADPGlutamine synthetase6.3.1.20.441
2rc3NADCBS domain/0.441
2znq401Peroxisome proliferator-activated receptor delta/0.441
3fln3FNMitogen-activated protein kinase 14/0.441
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.441
3p8iFMNPentaerythritol tetranitrate reductase/0.441
3w4yFADMitochondrial FAD-linked sulfhydryl oxidase ERV11.8.3.20.441
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
4gk3L87Ephrin type-A receptor 32.7.10.10.441
4jvmXDIEstrogen sulfotransferase2.8.2.40.441
4kq1U5PGlycogen [starch] synthase/0.441
4l9kEHFSerum albumin/0.441
1cjkFOKAdenylate cyclase type 2/0.440
1cjkFOKAdenylate cyclase type 5/0.440
1fxoTMPGlucose-1-phosphate thymidylyltransferase/0.440
1g1aNADdTDP-glucose 4,6-dehydratase/0.440
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.440
1m13HYFNuclear receptor subfamily 1 group I member 2/0.440
2bu9HFVIsopenicillin N synthase1.21.3.10.440
2etm7PYFocal adhesion kinase 12.7.10.20.440
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.440
2igoFADPyranose 2-oxidase/0.440
2xb5I7TTetracycline repressor protein class D/0.440
2y6o1N1Ephrin type-A receptor 42.7.10.10.440
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.440
3d8vUD1Bifunctional protein GlmU/0.440
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
3f883HTGlycogen synthase kinase-3 beta2.7.11.260.440
3fnlSHALactoperoxidase/0.440
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
3sayOFTGlycogen synthase kinase-3 beta2.7.11.260.440
4g2fC07Ephrin type-A receptor 32.7.10.10.440
4gu94GUFocal adhesion kinase 12.7.10.20.440
4ix4ADPUncharacterized protein/0.440