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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
3phjDHKShikimate dehydrogenase (NADP(+))

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3phjDHKShikimate dehydrogenase (NADP(+))/1.000
2hk9NAPShikimate dehydrogenase (NADP(+))/0.599
4bfzZVZPantothenate kinase2.7.1.330.501
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.493
2g1n1IGRenin3.4.23.150.493
3wqmB29Diterpene synthase3.1.7.80.489
2el0SAHDiphthine synthase/0.488
2e8qSAHDiphthine synthase/0.487
2emrSAHDiphthine synthase/0.487
4lol1YEStimulator of interferon genes protein/0.485
2dv4SAHDiphthine synthase/0.480
2ejzSAHDiphthine synthase/0.480
2ek7SAHDiphthine synthase/0.480
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.480
2cy0NAPShikimate dehydrogenase (NADP(+))/0.479
3h3qH13Collagen type IV alpha-3-binding protein/0.478
1wngSAHDiphthine synthase/0.477
1xddAAYIntegrin alpha-L/0.477
2dv3SAHDiphthine synthase/0.477
1je1GMPPurine nucleoside phosphorylase/0.476
1og4NAIT-cell ecto-ADP-ribosyltransferase 2/0.475
4bfxZVXPantothenate kinase2.7.1.330.474
2dxvSAHDiphthine synthase/0.473
1odjGMPPurine nucleoside phosphorylase/0.472
3q43D66M1 family aminopeptidase3.4.110.472
4iah1DXAlr2278 protein/0.472
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
2e8sSAHDiphthine synthase/0.470
2ejjSAHDiphthine synthase/0.470
4b4vL34Bifunctional protein FolD/0.470
4du82P0Mevalonate diphosphate decarboxylase/0.469
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.468
2dsgSAHDiphthine synthase/0.468
2eh5SAHDiphthine synthase/0.468
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.467
2el3SAHDiphthine synthase/0.467
2emuSAHDiphthine synthase/0.467
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.467
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4euaCOASuccinyl-CoA:acetate CoA-transferase/0.466
1t2cNAIL-lactate dehydrogenase1.1.1.270.465
2dekSAHDiphthine synthase/0.465
2i7nACOPantothenate kinase 12.7.1.330.465
3qe2FMNNADPH--cytochrome P450 reductase/0.465
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.464
2dxwSAHDiphthine synthase/0.464
2qimZEAClass 10 plant pathogenesis-related protein/0.464
2e8hSAHDiphthine synthase/0.463
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.463
2p5cSAHDiphthine synthase/0.463
2pcaSAHDiphthine synthase/0.463
4c0bATPmRNA cleavage and polyadenylation factor CLP1/0.463
4i1nFOLDihydrofolate reductase1.5.1.30.463
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
2pcmSAHDiphthine synthase/0.462
2qw034Z4-chlorobenzoyl CoA ligase/0.462
3h3r14HCollagen type IV alpha-3-binding protein/0.462
3in6FMNUncharacterized protein/0.462
3p0fBAUUridine phosphorylase 22.4.2.30.462
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.461
2hutSAHDiphthine synthase/0.461
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.461
4fxy0W2Neurolysin, mitochondrial3.4.24.160.461
3tjzGNPADP-ribosylation factor 1/0.460
2e08SAHDiphthine synthase/0.459
2rlcCHDCholoylglycine hydrolase3.5.1.240.459
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.459
3qt62P0Mevalonate diphosphate decarboxylase/0.459
1rfuADPPyridoxal kinase2.7.1.350.458
2ek2SAHDiphthine synthase/0.458
2g247IGRenin3.4.23.150.458
2gjlFMNNitronate monooxygenase1.13.12.160.458
2p2xSAHDiphthine synthase/0.458
2pciSAHDiphthine synthase/0.458
1tqf32PBeta-secretase 13.4.23.460.457
1vbiNADMalate/L-lactate dehydrogenase family protein/0.457
2ejkSAHDiphthine synthase/0.457
2eldSAHDiphthine synthase/0.457
2eleSAHDiphthine synthase/0.457
2en5SAHDiphthine synthase/0.457
2gv8NDPThiol-specific monooxygenase1.14.130.457
2huxSAHDiphthine synthase/0.457
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3rbaCODPhosphopantetheine adenylyltransferase/0.457
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.457
4rvgTYDD-mycarose 3-C-methyltransferase/0.457
1culFOKAdenylate cyclase type 2/0.456
1culFOKAdenylate cyclase type 5/0.456
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.456
2ed5SAHDiphthine synthase/0.456
2gtbAZPOrf1ab polyprotein/0.456
2ikuLIYRenin3.4.23.150.456
2pchSAHDiphthine synthase/0.456
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.456
4g7gVFVLanosterol 14-alpha-demethylase/0.456
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.455
3h3t16HCollagen type IV alpha-3-binding protein/0.455
3hl0NADMaleylacetate reductase/0.455
3v2uATPProtein GAL3/0.455
3vilSA0Beta-glucosidase/0.455
4guuFA9Lysine-specific histone demethylase 1B10.455
4i8zG08Gag-Pol polyprotein3.4.23.160.455
2egsSAHDiphthine synthase/0.454
2huvSAHDiphthine synthase/0.454
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.453
2e7rSAHDiphthine synthase/0.453
2g1s4IGRenin3.4.23.150.453
2owuSAHDiphthine synthase/0.453
2p5fSAHDiphthine synthase/0.453
2yj4ATPCopper-transporting ATPase/0.453
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.453
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3fr5I4AFatty acid-binding protein, adipocyte/0.453
3hk1B64Fatty acid-binding protein, adipocyte/0.453
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1xe65FPPlasmepsin-23.4.23.390.452
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.452
2p6iSAHDiphthine synthase/0.452
2p9dSAHDiphthine synthase/0.452
2pb5SAHDiphthine synthase/0.452
4dptAGSMevalonate diphosphate decarboxylase/0.452
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.452
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.452
1c7oPPGHemolysin/0.451
2ed3SAHDiphthine synthase/0.451
2eh4SAHDiphthine synthase/0.451
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.451
3mx5UTPNucleoprotein/0.451
3oqfS51Renin3.4.23.150.451
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.451
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.451
1cnfFADNitrate reductase [NADH]1.7.1.10.450
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.450
1xe55FEPlasmepsin-23.4.23.390.450
2huqSAHDiphthine synthase/0.450
3h3sH15Collagen type IV alpha-3-binding protein/0.450
4jyzATPGlutamine--tRNA ligase6.1.1.180.450
5irnADPNucleotide binding oligomerization domain containing 2/0.450
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.449
2bf4FMNNADPH--cytochrome P450 reductase/0.449
2e07SAHDiphthine synthase/0.449
3tr05GPGuanylate kinase/0.449
1rdwLARActin, alpha skeletal muscle/0.448
1w6hTITPlasmepsin-23.4.23.390.448
2a87FADThioredoxin reductase1.8.1.90.448
2dsiSAHDiphthine synthase/0.448
2dv7SAHDiphthine synthase/0.448
2eglSAHDiphthine synthase/0.448
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3l6jZ90Alr2278 protein/0.448
4bb3KKAIsopenicillin N synthase1.21.3.10.448
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.448
4lutDCSAlanine racemase/0.448
4rvfTYDD-mycarose 3-C-methyltransferase/0.448
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.447
2a5kAZPReplicase polyprotein 1ab3.4.220.447
2e17SAHDiphthine synthase/0.447
2eniSAHDiphthine synthase/0.447
2oapANPType II secretion system protein (GspE-2)/0.447
2r6gATPMaltose/maltodextrin import ATP-binding protein MalK/0.447
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.447
4a8v2ANMajor pollen allergen Bet v 1-J/0.447
4c717RD3-oxoacyl-ACP synthase/0.447
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.447
4ke11R6Beta-secretase 13.4.23.460.447
4m83ERYOleandomycin glycosyltransferase2.4.10.447
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.446
2dv5SAHDiphthine synthase/0.446
2ekaSAHDiphthine synthase/0.446
2i4qUA4Renin3.4.23.150.446
2jlbUDMUncharacterized protein/0.446
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.446
2p6lSAHDiphthine synthase/0.446
4b68NAPL-ornithine N(5)-monooxygenase/0.446
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.446
1nzdUPGDNA beta-glucosyltransferase/0.445
1obbNADAlpha-glucosidase3.2.1.200.445
1pqc444Oxysterols receptor LXR-beta/0.445
1vceSAHDiphthine synthase/0.445
2e15SAHDiphthine synthase/0.445
2pcgSAHDiphthine synthase/0.445
3mj4URMUDP-galactopyranose mutase/0.445
4egbNADdTDP-glucose 4,6-dehydratase/0.445
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.445
1cneFADNitrate reductase [NADH]1.7.1.10.444
1ypeUIPProthrombin3.4.21.50.444
2ab8MTPAdenosine kinase2.7.1.200.444
2bjfDXCCholoylglycine hydrolase3.5.1.240.444
2ea2F77Methionine aminopeptidase 2/0.444
2eeqSAHDiphthine synthase/0.444
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3aezGDPPantothenate kinase2.7.1.330.444
3pn1IVHDNA ligase/0.444
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.444
4bfwZVWPantothenate kinase2.7.1.330.444
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.444
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.444
1ebdFADDihydrolipoyl dehydrogenase1.8.1.40.443
1g1aNADdTDP-glucose 4,6-dehydratase/0.443
1j9zFADNADPH--cytochrome P450 reductase/0.443
1lbcCYZGlutamate receptor 2/0.443
2e8rSAHDiphthine synthase/0.443
2p6kSAHDiphthine synthase/0.443
2pb4SAHDiphthine synthase/0.443
2pb6SAHDiphthine synthase/0.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.443
3gwfNAPCyclohexanone monooxygenase/0.443
3jynNDPQuinone oxidoreductase/0.443
3vucHHERenin3.4.23.150.443
4zgsNADPutative D-lactate dehydrogenase/0.443
5agaANPDNA polymerase theta/0.443
5ejaTD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.443
1kh3ANPArgininosuccinate synthase/0.442
1pwuGM6Lethal factor3.4.24.830.442
1vikBAYGag-Pol polyprotein/0.442
1x2hLPALipoate-protein ligase A6.3.1.200.442
2egbSAHDiphthine synthase/0.442
2gjnFMNNitronate monooxygenase1.13.12.160.442
2uxoTACHTH-type transcriptional regulator TtgR/0.442
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.442
2vbdV10Isopenicillin N synthase1.21.3.10.442
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.442
3ed1GA3Gibberellin receptor GID1/0.442
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.442
3vyfVYFRenin3.4.23.150.442
4lh71X8DNA ligase/0.442
4xr9NADCalS8/0.442
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.441
2e4nSAHDiphthine synthase/0.441
2ek3SAHDiphthine synthase/0.441
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.441
2owgSAHDiphthine synthase/0.441
2p5uNADUDP-glucose 4-epimerase/0.441
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.441
3e6eDCSAlanine racemase/0.441
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.441
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.441
3vqsJT1Genome polyprotein/0.441
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.441
1vgqCAOFormyl-CoA:oxalate CoA-transferase/0.440
2dxxSAHDiphthine synthase/0.440
2jl1NAPTriphenylmethane reductase/0.440
3hnzPMN3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.440
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.440
4bfvZVVPantothenate kinase2.7.1.330.440
4jxrACOAcetyltransferase/0.440
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.440
5ej8TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.440