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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
2rgxAP5Adenylate kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2rgxAP5Adenylate kinase/1.000
4jl5ADPAdenylate kinase/0.674
4jl6ADPAdenylate kinase/0.593
4jkyADPAdenylate kinase/0.590
4cf7ADPAdenylate kinase/0.585
4jloADPAdenylate kinase/0.583
3dl0AP5Adenylate kinase/0.547
4w5jAP5Adenylate kinase/0.540
4x8lAP5Adenylate kinase/0.536
4qbiAP5Adenylate kinase/0.534
4jldADPAdenylate kinase/0.528
4nu0AP5Adenylate kinase/0.524
2osbAP5Adenylate kinase/0.520
2qajAP5Adenylate kinase/0.517
2akyAP5Adenylate kinase/0.511
2oo7AP5Adenylate kinase/0.505
2eckADPAdenylate kinase/0.504
2eu8AP5Adenylate kinase/0.503
4bb3KKAIsopenicillin N synthase1.21.3.10.503
3hpqAP5Adenylate kinase/0.502
3dkvAP5Adenylate kinase/0.496
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.493
1akeAP5Adenylate kinase/0.490
3tlxADPAdenylate kinase 2/0.490
4mkfAP5Adenylate kinase/0.490
1jpaANPEphrin type-B receptor 22.7.10.10.484
1p3jAP5Adenylate kinase/0.483
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.483
4x8oAP5Adenylate kinase/0.483
4g2fC07Ephrin type-A receptor 32.7.10.10.482
4ambDUDPutative glycosyl transferase/0.478
2wq6FADRE11660p/0.477
3mpt1GKMitogen-activated protein kinase 14/0.477
4qbhAP5Adenylate kinase/0.476
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.475
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.475
4mkhAP5Adenylate kinase/0.475
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.474
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.473
1zdwFLVPrenyltransferase/0.472
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.470
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.469
1hb3SCVIsopenicillin N synthase1.21.3.10.469
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.469
1bk0ACVIsopenicillin N synthase1.21.3.10.468
1p4aPCPPur operon repressor/0.468
2zb3NDPProstaglandin reductase 21.3.1.480.468
4zohFADPutative oxidoreductase FAD-binding subunit/0.468
2qo9ANPEphrin type-A receptor 32.7.10.10.467
1ankANPAdenylate kinase/0.466
1blzACVIsopenicillin N synthase1.21.3.10.466
1u59STUTyrosine-protein kinase ZAP-702.7.10.20.466
3d7zGK5Mitogen-activated protein kinase 14/0.466
1qiqACCIsopenicillin N synthase1.21.3.10.465
2bu9HFVIsopenicillin N synthase1.21.3.10.465
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.465
2vbdV10Isopenicillin N synthase1.21.3.10.465
3d8vUD1Bifunctional protein GlmU/0.465
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.464
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.464
2jb4A14Isopenicillin N synthase1.21.3.10.464
2bfmTOPPteridine reductase 11.5.1.330.463
2eixFADNADH-cytochrome b5 reductase/0.463
3adaNADSubunit alpha of sarocosine oxidase/0.463
3jq3ADPLombricine kinase/0.463
3zoiM2WIsopenicillin N synthase1.21.3.10.463
1rm4NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.461
1vjy460TGF-beta receptor type-12.7.11.300.461
2i4qUA4Renin3.4.23.150.461
2iviACWIsopenicillin N synthase1.21.3.10.461
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.461
4riyADPEpidermal growth factor receptor2.7.10.10.461
2ozuACOHistone acetyltransferase KAT6A/0.460
3a8wATPProtein kinase C iota type2.7.11.130.460
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
2c29NAPDihydroflavonol 4-reductase/0.459
2cgpCMPcAMP-activated global transcriptional regulator CRP/0.459
3t3r9PLCytochrome P450 2A61.14.130.459
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.458
2ylxFADPhenylacetone monooxygenase1.14.13.920.458
3bgxMEFThymidylate synthase/0.458
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.458
3cgbCOACoenzyme A disulfide reductase/0.458
4an4DUDPutative glycosyl transferase/0.458
1uzwCDHIsopenicillin N synthase1.21.3.10.457
2bakAQZMitogen-activated protein kinase 14/0.457
2dv4SAHDiphthine synthase/0.457
2e07SAHDiphthine synthase/0.457
3zkyWT4Isopenicillin N synthase1.21.3.10.457
4a9yAQZMitogen-activated protein kinase 14/0.457
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
4in44IDKelch-like ECH-associated protein 1/0.457
5iubCLRAdenosine receptor A2a/0.457
1kzjCB3Thymidylate synthase/0.456
3kb6NADD-lactate dehydrogenase/0.456
3p2oNADBifunctional protein FolD/0.456
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.456
4mkgAP5Adenylate kinase/0.456
4qms1N1Serine/threonine-protein kinase 242.7.11.10.456
2vdgNDPAldose reductase1.1.1.210.455
2y05NAPProstaglandin reductase 1/0.455
3etgNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.455
1hfqMOTDihydrofolate reductase1.5.1.30.454
2cduFADNADH oxidase/0.454
2gfsPQBMitogen-activated protein kinase 14/0.454
2wo7ASVIsopenicillin N synthase1.21.3.10.454
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.454
3itzP66Mitogen-activated protein kinase 14/0.454
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.454
4a81DXCMajor pollen allergen Bet v 1-A/0.454
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.453
1nzdUPGDNA beta-glucosyltransferase/0.453
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.453
3owj1ELCasein kinase II subunit alpha2.7.11.10.453
1cjtFOKAdenylate cyclase type 2/0.452
1cjtFOKAdenylate cyclase type 5/0.452
1dhiMTXDihydrofolate reductase1.5.1.30.452
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.452
1mp0NADAlcohol dehydrogenase class-31.1.1.10.452
1uykPUXHeat shock protein HSP 90-alpha/0.452
1v9aSAHUncharacterized protein/0.452
2bunFADAppA protein/0.452
3oibFDAPutative acyl-CoA dehydrogenase/0.452
4hjoAQ4Epidermal growth factor receptor2.7.10.10.452
1fwkADPHomoserine kinase2.7.1.390.451
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.451
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.451
2d3mCOA5,7-dihydroxy-2-methylchromone synthase2.3.1.2160.451
2itqITQEpidermal growth factor receptor2.7.10.10.451
2vn0TDZCytochrome P450 2C8/0.451
3rg9WRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.451
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.450
3eej53RUncharacterized protein/0.450
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.450
3lfcZ86Mitogen-activated protein kinase 14/0.450
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.450
4frkDWDBeta-secretase 13.4.23.460.450
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.449
3lsiFADPyranose 2-oxidase/0.449
3tqhNDPQuinone oxidoreductase/0.449
4lcjNADC-terminal-binding protein 2/0.449
1k0lFADp-hydroxybenzoate hydroxylase/0.448
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
1stcSTUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
1tqf32PBeta-secretase 13.4.23.460.448
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2w02ATPAcsD/0.448
2zm4KSMTyrosine-protein kinase Lck2.7.10.20.448
3sf6FDAGlutaryl-CoA dehydrogenase/0.448
3u8k09PAcetylcholine-binding protein/0.448
4fxfATPPyruvate kinase PKM2.7.1.400.448
4uymVOR14-alpha sterol demethylase Cyp51B/0.448
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.448
5iu86DZAdenosine receptor A2a/0.448
1nhhANPDNA mismatch repair protein MutL/0.447
1u3dFADCryptochrome-1/0.447
2xvv9DNSerum albumin/0.447
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3flzFLZMitogen-activated protein kinase 14/0.447
3oqfS51Renin3.4.23.150.447
3p3zP3ZPutative cytochrome P450/0.447
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.447
1fmlRTLRetinol dehydratase/0.446
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.446
2rhrEMOPutative ketoacyl reductase1.3.10.446
3ieuGDPGTPase Era/0.446
3jynNDPQuinone oxidoreductase/0.446
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.446
4fqsLYAThymidylate synthase ThyA/0.446
4hxyNDPPlm1/0.446
4kl9NDPDihydrofolate reductase1.5.1.30.446
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.446
8catNDPCatalase1.11.1.60.446
5k2dZMAAdenosine receptor A2a/0.446
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.445
1qy5NECEndoplasmin/0.445
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.445
2x0rNADMalate dehydrogenase/0.445
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.445
3lqfNADGalactitol dehydrogenase/0.445
3mvm39PMitogen-activated protein kinase 14/0.445
4auxXTCTetracycline repressor protein class D/0.445
4jb1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.445
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.445
4xguADPPutative pachytene checkpoint protein 2/0.445
1ezvUQ6Cytochrome b/0.444
1uycPU7Heat shock protein HSP 90-alpha/0.444
2b7aIZATyrosine-protein kinase JAK2/0.444
2om9AJAPeroxisome proliferator-activated receptor gamma/0.444
2vcmM11Isopenicillin N synthase1.21.3.10.444
2wd4TBVAscorbate peroxidase/0.444
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3a783EVVitamin D3 receptor/0.444
3d0bSNXHeat shock protein HSP 90-alpha/0.444
3drcMTXDihydrofolate reductase1.5.1.30.444
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
3l0lHC3Nuclear receptor ROR-gamma/0.444
3mw9NAIGlutamate dehydrogenase 1, mitochondrial1.4.1.30.444
3raiX85Cyclin-dependent kinase 22.7.11.220.444
4xznNAPAldo-keto reductase family 1 member B101.1.10.444
7catNDPCatalase1.11.1.60.444
1gc5ADPADP-dependent glucokinase2.7.1.1470.443
1h74ADPHomoserine kinase2.7.1.390.443
1uyhPU0Heat shock protein HSP 90-alpha/0.443
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.443
1zrzBI1Protein kinase C iota type2.7.11.130.443
2bjhFERFeruloyl esterase A3.1.1.730.443
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.443
2ejzSAHDiphthine synthase/0.443
2fszOHTEstrogen receptor beta/0.443
2oorNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.443
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.443
3bkbSTUTyrosine-protein kinase Fes/Fps2.7.10.20.443
3cbsR12Cellular retinoic acid-binding protein 2/0.443
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.443
3mjrAC2Deoxycytidine kinase2.7.1.740.443
3uwlFOZThymidylate synthase/0.443
3wb2YGPUncharacterized protein MJ0488/0.443
4ki8ADP60 kDa chaperonin/0.443
4mgkCMPRap guanine nucleotide exchange factor 4/0.443
5uviZMAAdenosine receptor A2a/0.443
1bwsNDPGDP-L-fucose synthase/0.442
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
1g1aNADdTDP-glucose 4,6-dehydratase/0.442
1xddAAYIntegrin alpha-L/0.442
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.442
2j83BATUlilysin3.4.240.442
2qo7ANPEphrin type-A receptor 32.7.10.10.442
2y3rTRKTamL/0.442
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
4dpy2P0Mevalonate diphosphate decarboxylase/0.442
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.441
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.441
1pr9NAPL-xylulose reductase1.1.1.100.441
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.441
3bbrBHYGlutamate receptor 2/0.441
3cblSTUTyrosine-protein kinase Fes/Fps2.7.10.20.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3fhxPXLPyridoxal kinase2.7.1.350.441
4b722FBBeta-secretase 13.4.23.460.441
4qxq1YEStimulator of interferon genes protein/0.441
4zm3PLPAminotransferase/0.441
5iu4ZMAAdenosine receptor A2a/0.441
1a2nTETUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
1osvCHCBile acid receptor/0.440
1pd9CO4Dihydrofolate reductase1.5.1.30.440
1qpdSTUTyrosine-protein kinase Lck2.7.10.20.440
1rfuADPPyridoxal kinase2.7.1.350.440
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.440
2bueCOAAAC(6')-Ib/0.440
2d52COA5,7-dihydroxy-2-methylchromone synthase2.3.1.2160.440
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.440
2ofv242Tyrosine-protein kinase Lck2.7.10.20.440
2vnkFADNADPH:ferredoxin reductase/0.440
2w3wVG9Dihydrofolate reductase/0.440
3ac3KSHTyrosine-protein kinase Lck2.7.10.20.440
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.440
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.440
4gk3L87Ephrin type-A receptor 32.7.10.10.440