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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2q5yTYR_GLY_LEUNuclear pore complex protein Nup98-Nup96

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2q5yTYR_GLY_LEUNuclear pore complex protein Nup98-Nup96/1.000
3sxjSAMPutative methyltransferase/0.488
1g63FMNEpidermin decarboxylase4.1.10.483
2z95NDPGDP-mannose 4,6-dehydratase/0.478
3cvkN34Genome polyprotein2.7.7.480.478
1qx4FADNADH-cytochrome b5 reductase 31.6.2.20.472
2dvmNAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme]/0.469
2r5nTPPTransketolase 1/0.469
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
2xlpFADPutative flavin-containing monooxygenase/0.468
5erm210Fusicoccadiene synthase4.2.3.430.468
4isg1FYGlucokinase2.7.1.20.467
2r8oT5XTransketolase 1/0.466
3qt62P0Mevalonate diphosphate decarboxylase/0.466
1cneFADNitrate reductase [NADH]1.7.1.10.465
1me6IVSPlasmepsin-23.4.23.390.465
2fznFADBifunctional protein PutA1.5.5.20.464
2r8pT6FTransketolase 1/0.464
3ingNDPHomoserine dehydrogenase related protein/0.464
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.464
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.463
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.463
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.463
3a25SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.462
3phiNDPShikimate dehydrogenase (NADP(+))/0.462
1rf7DHFDihydrofolate reductase1.5.1.30.460
4fpy0V8Sialidase B3.2.1.180.460
4ise1FWGlucokinase2.7.1.20.460
2xvhFADPutative flavin-containing monooxygenase/0.459
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.459
3h3qH13Collagen type IV alpha-3-binding protein/0.459
1gpuTHDTransketolase 12.2.1.10.458
3gxfIFMGlucosylceramidase3.2.1.450.458
1bim0QBRenin3.4.23.150.457
2p5cSAHDiphthine synthase/0.457
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.457
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.456
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.456
2pchSAHDiphthine synthase/0.455
2yexYEXSerine/threonine-protein kinase Chk12.7.11.10.455
3adaNADSubunit alpha of sarocosine oxidase/0.455
3oogYTPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
2aouCQAHistamine N-methyltransferase2.1.1.80.454
2dsiSAHDiphthine synthase/0.454
2ejzSAHDiphthine synthase/0.454
2hfuMEVMevalonate kinase/0.454
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.454
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.454
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
2zw5COABleomycin acetyltransferase/0.454
3p62FMNPentaerythritol tetranitrate reductase/0.454
3udq09EBeta-secretase 13.4.23.460.454
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.453
2cndFADNitrate reductase [NADH]1.7.1.10.453
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.453
4b0532DBeta-secretase 13.4.23.460.453
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.452
2ccu2D9Heat shock protein HSP 90-alpha/0.452
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.452
2xlrFADPutative flavin-containing monooxygenase/0.452
3rtnRTNBeta-secretase 13.4.23.460.452
5kwvANPPantothenate synthetase/0.452
2vq7NAPPutative flavin-containing monooxygenase/0.451
3r2fPB0Beta-secretase 13.4.23.460.451
1ra3MTXDihydrofolate reductase1.5.1.30.450
2d5nNDPRiboflavin biosynthesis protein RibD1.1.1.1930.450
2huxSAHDiphthine synthase/0.450
2qrqS13Glycogen phosphorylase, muscle form2.4.1.10.450
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.450
4c04SFGProtein arginine N-methyltransferase 6/0.450
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.450
4dch4DCGlucokinase2.7.1.20.449
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.449
4g8jTHMUridine phosphorylase/0.449
4hhy15RPoly [ADP-ribose] polymerase 12.4.2.300.449
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.448
3bm1FMNPutative NAD(P)H nitroreductase YdjA/0.448
1wn3HXCPhenylacetic acid degradation protein PaaI/0.447
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.447
3duyAFJBeta-secretase 13.4.23.460.447
3wqmB29Diterpene synthase3.1.7.80.447
4g6oE28Mitogen-activated protein kinase 12.7.11.240.447
4qnuGEKtRNA U34 carboxymethyltransferase/0.447
1umkFADNADH-cytochrome b5 reductase 31.6.2.20.446
1xe65FPPlasmepsin-23.4.23.390.446
1xuoLA1Integrin alpha-L/0.446
2c29NAPDihydroflavonol 4-reductase/0.446
2gtbAZPOrf1ab polyprotein/0.446
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.446
1d0mBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.445
1i75NOJCyclomaltodextrin glucanotransferase2.4.1.190.445
1thyUMPThymidylate synthase/0.445
2ekaSAHDiphthine synthase/0.445
3h5sH5SGenome polyprotein2.7.7.480.445
3veu0GOBeta-secretase 13.4.23.460.445
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.445
2cgx3D3Serine/threonine-protein kinase Chk12.7.11.10.444
2e8qSAHDiphthine synthase/0.444
3bwjARXcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1ay0TPPTransketolase 12.2.1.10.443
1odcA8BAcetylcholinesterase3.1.1.70.443
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.443
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.443
3h3r14HCollagen type IV alpha-3-binding protein/0.443
3qiyQI1Botulinum neurotoxin type A3.4.24.690.443
3qviK95HAP protein/0.443
4hh4SAHCcbJ/0.443
4q0kGA3Phytohormone-binding protein/0.443
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.443
1h51FMNPentaerythritol tetranitrate reductase/0.442
1umcTDP2-oxoisovalerate dehydrogenase subunit alpha1.2.4.40.442
1umcTDP2-oxoisovalerate dehydrogenase subunit beta1.2.4.40.442
2bqzSAHN-lysine methyltransferase KMT5A/0.442
2zvbSAHPrecorrin-3 C17-methyltransferase/0.442
3orfNADDihydropteridine reductase1.5.1.340.442
3t3q9PLCytochrome P450 2A61.14.130.442
3zksWZVBeta-secretase 23.4.23.450.442
4dro0MDPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.442
4wxg2BOSerine hydroxymethyltransferase/0.442
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.442
1dpmEBPParathion hydrolase3.1.8.10.441
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.441
1j49NADD-lactate dehydrogenase1.1.1.280.441
1sbzFMNProbable UbiX-like flavin prenyltransferase/0.441
2b8tTHMThymidine kinase/0.441
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.441
2zsaADPPantothenate kinase2.7.1.330.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3ggoNAIPrephenate dehydrogenase/0.441
3n0tOPYDipeptidyl peptidase 23.4.14.20.441
3p8hP8HLethal(3)malignant brain tumor-like protein 1/0.441
4a8v2ANMajor pollen allergen Bet v 1-J/0.441
4b69FADL-ornithine N(5)-monooxygenase/0.441
4j1k1HGBeta-secretase 13.4.23.460.441
4djhJDCKappa-type opioid receptor/0.441
1rz1NADPhenol 2-hydroxylase component B/0.440
1wngSAHDiphthine synthase/0.440
2c20NADUDP-glucose 4-epimerase/0.440
2dv3SAHDiphthine synthase/0.440
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.440
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.440
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.440
3juqAJDPhenazine biosynthesis protein A/B/0.440
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.440
3zhyFM61-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
3zpqXF5Beta-1 adrenergic receptor/0.440
4jzr4JREgl nine homolog 1/0.440
4qmzB49Serine/threonine-protein kinase 242.7.11.10.440
5f59SAHHistone-lysine N-methyltransferase 2C2.1.1.430.440