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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
3iktNADRedox-sensing transcriptional repressor Rex

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3iktNADRedox-sensing transcriptional repressor Rex/1.000
3rsv3RSBeta-secretase 13.4.23.460.505
2ab8MTPAdenosine kinase2.7.1.200.503
1x8lOXRRetinol dehydratase/0.502
3vf60H6Glucokinase2.7.1.20.497
4bftZVTPantothenate kinase2.7.1.330.488
4cdmFO1Deoxyribodipyrimidine photolyase/0.487
4bfxZVXPantothenate kinase2.7.1.330.483
2a9z26AAdenosine kinase2.7.1.200.480
2lfoGCHFatty acid-binding protein, liver/0.480
1s7gNADNAD-dependent protein deacylase 2/0.479
1yhjR6CPyridoxal kinase2.7.1.350.479
3rtnRTNBeta-secretase 13.4.23.460.479
5dozNDPJamJ/0.478
1xddAAYIntegrin alpha-L/0.476
3k1wBFXRenin3.4.23.150.476
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.476
3q9bB3NAcetylpolyamine amidohydrolase/0.476
3g70A5TRenin3.4.23.150.474
3keqNADRedox-sensing transcriptional repressor Rex/0.473
3oadLPORenin3.4.23.150.472
1icqOPD12-oxophytodienoate reductase 11.3.1.420.471
1g63FMNEpidermin decarboxylase4.1.10.470
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.470
3pm1ETHTH-type transcriptional regulator QacR/0.468
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3s41S41Glucokinase2.7.1.20.466
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.466
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.465
1pkfEPDEpothilone C/D epoxidase1.140.464
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.464
4bfuZVUPantothenate kinase2.7.1.330.464
3pqbVGPPutative oxidoreductase/0.463
3s3vTOPDihydrofolate reductase1.5.1.30.463
4bfsZVSPantothenate kinase2.7.1.330.463
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.463
4b4w9L9Bifunctional protein FolD/0.462
4dbc3QPAspartate aminotransferase2.6.1.10.461
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.460
3br3ETHTH-type transcriptional regulator QacR/0.460
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.460
4b4vL34Bifunctional protein FolD/0.460
2ejzSAHDiphthine synthase/0.459
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.459
3fr4F8AFatty acid-binding protein, adipocyte/0.459
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.458
4uymVOR14-alpha sterol demethylase Cyp51B/0.458
2vbdV10Isopenicillin N synthase1.21.3.10.457
2gpjFADSiderophore-interacting protein/0.456
3gwfNAPCyclohexanone monooxygenase/0.456
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
1yc2NADNAD-dependent protein deacylase 2/0.455
2q153MRBeta-secretase 13.4.23.460.455
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.454
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.454
5dp2NAPCurF/0.454
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.453
1zg32HIIsoflavone 4'-O-methyltransferase/0.453
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
2w6zL21Biotin carboxylase6.3.4.140.452
3h1vTK1Glucokinase2.7.1.20.452
3ihgVAKAklavinone 12-hydroxylase RdmE/0.452
3oagLPQRenin3.4.23.150.452
4zzjCNANAD-dependent protein deacetylase sirtuin-13.5.10.452
1dr4HBIDihydrofolate reductase1.5.1.30.451
1yw8A75Methionine aminopeptidase 2/0.451
2a5kAZPReplicase polyprotein 1ab3.4.220.451
3fr5I4AFatty acid-binding protein, adipocyte/0.451
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.451
5bn3ADPV-type ATP synthase alpha chain/0.451
5bn3ADPNEQ263/0.451
1blzACVIsopenicillin N synthase1.21.3.10.450
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.450
3af1GDPPantothenate kinase2.7.1.330.450
3hl0NADMaleylacetate reductase/0.450
3zoiM2WIsopenicillin N synthase1.21.3.10.450
1hfqMOTDihydrofolate reductase1.5.1.30.449
2a9y26AAdenosine kinase2.7.1.200.449
2x7hPFNProstaglandin reductase 310.449
3b9oFMNAlkane monoxygenase/0.449
1fmlRTLRetinol dehydratase/0.448
1qv0CZHObelin/0.448
1rpwDIDHTH-type transcriptional regulator QacR/0.448
2oegUPGUDP-glucose pyrophosphorylase/0.448
2uxhQUEHTH-type transcriptional regulator TtgR/0.448
4frkDWDBeta-secretase 13.4.23.460.448
4h3g10QBeta-secretase 13.4.23.460.448
1e79ATPATP synthase subunit alpha, mitochondrial/0.447
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.447
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.447
3gncQQQGlutaryl-CoA dehydrogenase/0.447
1bk0ACVIsopenicillin N synthase1.21.3.10.446
2dftADPShikimate kinase2.7.1.710.446
2z3uCRRCytochrome P450/0.446
3cb2GDPTubulin gamma-1 chain/0.446
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.446
3fhxPLPPyridoxal kinase2.7.1.350.446
3iw1ASDSteroid C26-monooxygenase1.14.13.1410.446
4b78KGGBeta-secretase 13.4.23.460.446
4iwv1J9Glucokinase2.7.1.20.446
2gevCOKPantothenate kinase2.7.1.330.445
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.445
2uxoTACHTH-type transcriptional regulator TtgR/0.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
3ielU5PRibonuclease TTHA02523.10.445
4iae1DXAlr2278 protein/0.445
2bxqIMNSerum albumin/0.444
2getCOKPantothenate kinase2.7.1.330.444
3g72A6TRenin3.4.23.150.444
3jynNDPQuinone oxidoreductase/0.444
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.444
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.444
5c1mCLRMu-type opioid receptor/0.444
1hb1OCVIsopenicillin N synthase1.21.3.10.443
1jdzFMBPurine nucleoside phosphorylase/0.443
1l2tATPUncharacterized ABC transporter ATP-binding protein MJ0796/0.443
1sm4FADFerredoxin--NADP reductase/0.443
2gv8NDPThiol-specific monooxygenase1.14.130.443
2zb8IMNProstaglandin reductase 21.3.1.480.443
3u8hBHPPhospholipase A2, membrane associated/0.443
4bfvZVVPantothenate kinase2.7.1.330.443
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.443
1dhfFOLDihydrofolate reductase1.5.1.30.442
2iviACWIsopenicillin N synthase1.21.3.10.442
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.442
3l63CAMCamphor 5-monooxygenase1.14.15.10.442
3l6jZ90Alr2278 protein/0.442
3sl2ATPSensor histidine kinase WalK/0.442
1oc1ASVIsopenicillin N synthase1.21.3.10.441
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
4azy7F3Beta-secretase 13.4.23.460.441
4iah1DXAlr2278 protein/0.441
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.441
1dr3HBIDihydrofolate reductase1.5.1.30.440
1je1GMPPurine nucleoside phosphorylase/0.440
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.440
3t3r9PLCytochrome P450 2A61.14.130.440
4bfwZVWPantothenate kinase2.7.1.330.440
4h1e10JBeta-secretase 13.4.23.460.440
4m2bUPGUDP-glucose pyrophosphorylase/0.440
5hs1VORLanosterol 14-alpha demethylase/0.440