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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
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.11.000
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.506
1rfvADPPyridoxal kinase2.7.1.350.492
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.488
3fhyATPPyridoxal kinase2.7.1.350.482
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.481
2bjfDXCCholoylglycine hydrolase3.5.1.240.478
3hl0NADMaleylacetate reductase/0.478
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.477
2yxuATPPyridoxal kinase2.7.1.350.476
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.476
4m83ERYOleandomycin glycosyltransferase2.4.10.476
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.475
5kwvANPPantothenate synthetase/0.473
2gjlFMNNitronate monooxygenase1.13.12.160.472
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.472
1xddAAYIntegrin alpha-L/0.471
4du82P0Mevalonate diphosphate decarboxylase/0.471
4a83DXCMajor pollen allergen Bet v 1-A/0.470
1w6hTITPlasmepsin-23.4.23.390.469
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.469
4a81DXCMajor pollen allergen Bet v 1-A/0.469
2iyfERYOleandomycin glycosyltransferase2.4.10.468
3tjzGNPADP-ribosylation factor 1/0.468
3k5c0BIBeta-secretase 13.4.23.460.464
2zsaADPPantothenate kinase2.7.1.330.463
3gqvNAPEnoyl reductase LovC10.463
3nsh957Beta-secretase 13.4.23.460.463
4i0i957Beta-secretase 13.4.23.460.463
2he5NDPAldo-keto reductase family 1 member C211.1.10.462
2iqgF2IBeta-secretase 13.4.23.460.461
3af0GDPPantothenate kinase2.7.1.330.461
3hyoADPPyridoxal kinase/0.461
2givACOHistone acetyltransferase KAT8/0.460
1eq2NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.459
1psa0ZLPepsin A3.4.23.10.459
2ahrNAPPyrroline-5-carboxylate reductase/0.459
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.459
1egdFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.458
1tqf32PBeta-secretase 13.4.23.460.458
2rlcCHDCholoylglycine hydrolase3.5.1.240.458
3h86AP5Adenylate kinase/0.458
3u9eCOALmo1369 protein/0.458
1xe55FEPlasmepsin-23.4.23.390.457
3i0pNADMalate dehydrogenase, putative/0.457
3lpiZ74Beta-secretase 13.4.23.460.457
3phiNDPShikimate dehydrogenase (NADP(+))/0.457
5fl3ADPPili retraction protein PilT/0.457
1t2cNAIL-lactate dehydrogenase1.1.1.270.456
2b4rAESGlyceraldehyde-3-phosphate dehydrogenase/0.456
3af1GDPPantothenate kinase2.7.1.330.456
3clrFADElectron transfer flavoprotein subunit alpha/0.456
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3ieuGDPGTPase Era/0.456
3ohh3HHBeta-secretase 13.4.23.460.456
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
5ftcADPTPR domain protein/0.456
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
3pfdFDAAcyl-CoA dehydrogenase FadE25/0.455
1me6IVSPlasmepsin-23.4.23.390.454
2dftADPShikimate kinase2.7.1.710.454
2ebaFADPutative glutaryl-CoA dehydrogenase/0.454
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.454
3clsFADElectron transfer flavoprotein subunit alpha/0.454
3keuATPPyridoxal kinase2.7.1.350.454
2ikuLIYRenin3.4.23.150.453
2z1mNDPGDP-mannose 4,6-dehydratase/0.453
4b65FADL-ornithine N(5)-monooxygenase/0.453
4f9fGDPPutative glycosyltransferase/0.453
2g8yNADHydroxycarboxylate dehydrogenase B/0.452
4bfxZVXPantothenate kinase2.7.1.330.452
4eb7PLPCysteine desulfurase IscS 2/0.452
4emtC2EStimulator of interferon genes protein/0.452
4esoNAPPutative oxidoreductase/0.452
1rfuADPPyridoxal kinase2.7.1.350.451
1udbUFGUDP-glucose 4-epimerase5.1.3.20.451
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.451
2oapANPType II secretion system protein (GspE-2)/0.451
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.451
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.451
3ge6FMNNitroreductase/0.451
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.451
4ambDUDPutative glycosyl transferase/0.451
4egbNADdTDP-glucose 4,6-dehydratase/0.451
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.450
2pg0FADAcyl-CoA dehydrogenase/0.450
3gvhNADMalate dehydrogenase/0.450
3kkzSAMUncharacterized protein/0.450
4ewo996Beta-secretase 13.4.23.460.450
4g7gVFVLanosterol 14-alpha-demethylase/0.450
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.450
4loi1YCStimulator of interferon genes protein/0.450
5jscFADPutative acyl-CoA dehydrogenase/0.450
2g1s4IGRenin3.4.23.150.449
2xfiXFIBeta-secretase 13.4.23.460.449
2yj5ATPCopper-transporting ATPase/0.449
3cic316Beta-secretase 13.4.23.460.449
3gw9VNILanosterol 14-alpha-demethylase/0.449
3uylTYDProbable NDP-rhamnosyltransferase/0.449
1eveE20Acetylcholinesterase3.1.1.70.448
1yb5NAPQuinone oxidoreductase1.6.5.50.448
2y0mACOHistone acetyltransferase KAT8/0.448
3cluFADElectron transfer flavoprotein subunit alpha/0.448
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3g70A5TRenin3.4.23.150.448
3nxxNDPDihydrofolate reductase1.5.1.30.448
3tr05GPGuanylate kinase/0.448
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.448
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.448
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.448
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.447
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.447
2i4qUA4Renin3.4.23.150.447
2j83BATUlilysin3.4.240.447
3a3gDLZLumazine protein/0.447
3adaNADSubunit alpha of sarocosine oxidase/0.447
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3mauEXTPutative sphingosine-1-phosphate lyase/0.447
3qlsNDPDihydrofolate reductase1.5.1.30.447
3zcsCAWGlycogen phosphorylase, muscle form2.4.1.10.447
4gavFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.447
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.447
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.446
1z7yAA5Cysteine synthase 12.5.1.470.446
2uzfCAA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.446
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.446
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3isjA8DPantothenate synthetase6.3.2.10.446
3lqfNADGalactitol dehydrogenase/0.446
4ddhMS0Pantothenate synthetase6.3.2.10.446
4g3jVNTLanosterol 14-alpha-demethylase/0.446
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4jldADPAdenylate kinase/0.446
4oqyNDP(S)-imine reductase/0.446
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.445
1obnASVIsopenicillin N synthase1.21.3.10.445
1rneC60Renin3.4.23.150.445
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.445
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.445
4blsAPCNTPase P4/0.445
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2i7pACOPantothenate kinase 32.7.1.330.444
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.444
2vkvTDCTetracycline repressor protein class D/0.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3aezGDPPantothenate kinase2.7.1.330.444
3dl0AP5Adenylate kinase/0.444
4b78KGGBeta-secretase 13.4.23.460.444
4bfzZVZPantothenate kinase2.7.1.330.444
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.444
4fm80UQBeta-secretase 13.4.23.460.444
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.444
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.444
4pzrCOAHistone acetyltransferase p300/0.444
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.444
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.443
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
2vkeTACTetracycline repressor protein class D/0.443
3csoXNIGenome polyprotein2.7.7.480.443
4bfsZVSPantothenate kinase2.7.1.330.443
4ipw1G7Mycocyclosin synthase1.14.21.90.443
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.443
4y9qC2EUncharacterized protein/0.443
1necFMNOxygen-insensitive NAD(P)H nitroreductase10.442
1s64778Geranylgeranyl transferase type-1 subunit beta2.5.1.590.442
2hrbNAPCarbonyl reductase [NADPH] 31.1.1.1840.442
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.442
3duyAFJBeta-secretase 13.4.23.460.442
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3imgBZ2Pantothenate synthetase6.3.2.10.442
4b0qGMFBeta-secretase 13.4.23.460.442
5irnADPNucleotide binding oligomerization domain containing 2/0.442
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kqbFMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.441
2g226IGRenin3.4.23.150.441
2xtnGTPGTPase IMAP family member 2/0.441
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.441
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4jloADPAdenylate kinase/0.441
4kgkGTPUncharacterized protein/0.441
4tm1FDAKtzI/0.441
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.440
2omeNADC-terminal-binding protein 2/0.440
2x86NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.440
3f63GTXGlutathione transferase GST1-4/0.440
3k1wBFXRenin3.4.23.150.440
4acxS8ZBeta-secretase 13.4.23.460.440
4bb3KKAIsopenicillin N synthase1.21.3.10.440
4xguADPPutative pachytene checkpoint protein 2/0.440