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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
1pu9COAHAT A1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1pu9COAHAT A1/1.000
1qsnCOAHAT A1/0.607
1puaCOAHAT A1/0.568
1cm0COAHistone acetyltransferase KAT2B2.3.1.480.516
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.505
4bfxZVXPantothenate kinase2.7.1.330.493
5kf2ACOPredicted acetyltransferase/0.489
3eksCY9Actin-5C/0.484
4uugPXGBranched-chain amino acid aminotransferase, putative/0.484
3ekuCY9Actin-5C/0.480
5cc9DDFDihydrofolate reductase1.5.1.30.480
4fhd0TTSpore photoproduct lyase/0.477
4oztP1AEcdysone receptor, putative/0.477
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.476
1b2lNDCAlcohol dehydrogenase1.1.1.10.472
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.472
2zsbADPPantothenate kinase2.7.1.330.472
1mewXMPInosine-5'-monophosphate dehydrogenase/0.471
3af1GDPPantothenate kinase2.7.1.330.471
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.470
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.470
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.469
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.469
3fhxPLPPyridoxal kinase2.7.1.350.467
1pq944BOxysterols receptor LXR-beta/0.466
2cjfRP43-dehydroquinate dehydratase4.2.1.100.466
2e0nSAHPrecorrin-2 C20-methyltransferase/0.465
3otwCOAPhosphopantetheine adenylyltransferase/0.465
4bftZVTPantothenate kinase2.7.1.330.465
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.464
3fr5I4AFatty acid-binding protein, adipocyte/0.464
1z7yAA5Cysteine synthase 12.5.1.470.463
4b4w9L9Bifunctional protein FolD/0.463
1obnASVIsopenicillin N synthase1.21.3.10.462
1xs7MMIBeta-secretase 13.4.23.460.462
2pncCLUPrimary amine oxidase, liver isozyme/0.462
2zs8ADPPantothenate kinase2.7.1.330.462
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3pftFMNFlavin reductase/0.462
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.462
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.462
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.461
5kgjACOPredicted acetyltransferase/0.461
3d2mCOAAmino-acid acetyltransferase/0.460
4bb3KKAIsopenicillin N synthase1.21.3.10.460
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.459
3exo5MSBeta-secretase 13.4.23.460.459
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
4b4vL34Bifunctional protein FolD/0.459
4bfvZVVPantothenate kinase2.7.1.330.459
4i1c1BEBeta-secretase 13.4.23.460.459
3fsjD7KBenzoylformate decarboxylase4.1.1.70.458
5kf8ACOPredicted acetyltransferase/0.458
1svmATPLarge T antigen3.6.40.457
2zevIPEGeranylgeranyl pyrophosphate synthase/0.457
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.457
4j0v1H7Beta-secretase 13.4.23.460.457
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.456
4n4v2GYTankyrase-12.4.2.300.456
4y1bNAPAntE/0.456
1trgCB3Thymidylate synthase/0.455
1txtCAAHMG-CoA synthase/0.455
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
2zsdCOAPantothenate kinase2.7.1.330.455
3fktSIIBeta-secretase 13.4.23.460.455
4gutFADLysine-specific histone demethylase 1B10.455
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.455
1hfqMOTDihydrofolate reductase1.5.1.30.454
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2g1n1IGRenin3.4.23.150.454
3ohh3HHBeta-secretase 13.4.23.460.454
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.454
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.453
1lkeDOGBilin-binding protein/0.453
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.453
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.453
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.453
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
2a2xNA9Prothrombin3.4.21.50.452
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.452
2hizLIJBeta-secretase 13.4.23.460.452
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.452
3vf60H6Glucokinase2.7.1.20.452
1h50FMNPentaerythritol tetranitrate reductase/0.451
1nm6L86Prothrombin3.4.21.50.451
2xviFADPutative flavin-containing monooxygenase/0.451
3h2sNDPPutative NADH-flavin reductase/0.451
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.451
2ejzSAHDiphthine synthase/0.450
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.450
2geuCOKPantothenate kinase2.7.1.330.450
2va7C27Beta-secretase 13.4.23.460.450
2vbpVB1Isopenicillin N synthase1.21.3.10.450
3nn6HNK6-hydroxy-L-nicotine oxidase/0.450
4dvi2IWTankyrase-12.4.2.300.450
1a9cGTPGTP cyclohydrolase 13.5.4.160.449
1wuaAP8Actin, alpha skeletal muscle/0.449
3udq09EBeta-secretase 13.4.23.460.449
4n1gCEIObelin/0.449
5kf9ACOPredicted acetyltransferase/0.449
3emlZMAAdenosine receptor A2a/0.449
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
1umcTDP2-oxoisovalerate dehydrogenase subunit alpha1.2.4.40.448
1umcTDP2-oxoisovalerate dehydrogenase subunit beta1.2.4.40.448
2vcmM11Isopenicillin N synthase1.21.3.10.448
3elm24FCollagenase 33.4.240.448
3oetNADErythronate-4-phosphate dehydrogenase/0.448
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4r1lADPPhenylacetate-coenzyme A ligase/0.448
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.448
1n5vNOMActVA 6 protein/0.447
1p0pBCHCholinesterase3.1.1.80.447
1qjfACSIsopenicillin N synthase1.21.3.10.447
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.447
2xvq9DSSerum albumin/0.447
2zsaADPPantothenate kinase2.7.1.330.447
3bgxMEFThymidylate synthase/0.447
3juqAJDPhenazine biosynthesis protein A/B/0.447
3rsv3RSBeta-secretase 13.4.23.460.447
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.447
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2hxzH7JCathepsin S3.4.22.270.446
2ou2ACOHistone acetyltransferase KAT5/0.446
2vjmCOAFormyl-CoA:oxalate CoA-transferase/0.446
3aezGDPPantothenate kinase2.7.1.330.446
4dbs0HVAldo-keto reductase family 1 member C3/0.446
4g8jTHMUridine phosphorylase/0.446
2gjnFMNNitronate monooxygenase1.13.12.160.445
3cb2GDPTubulin gamma-1 chain/0.445
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.445
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.445
4j0z1H5Beta-secretase 13.4.23.460.445
4zqcF6FTryptophan synthase alpha chain/0.445
1p5rCOAFormyl-CoA:oxalate CoA-transferase/0.444
1r2jFADFkbI/0.444
2givACOHistone acetyltransferase KAT8/0.444
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.444
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4d89BXDBeta-secretase 13.4.23.460.444
4q71FADBifunctional protein PutA/0.444
4zj8SUVOrexin receptor type 1/0.444
1hb3SCVIsopenicillin N synthase1.21.3.10.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.443
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.443
2z4y252Geranylgeranyl pyrophosphate synthase/0.443
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.443
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.443
3lpiZ74Beta-secretase 13.4.23.460.443
3p0fBAUUridine phosphorylase 22.4.2.30.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4j1f1HLBeta-secretase 13.4.23.460.443
4k28NADShikimate dehydrogenase family protein/0.443
1blzACVIsopenicillin N synthase1.21.3.10.442
1gky5GPGuanylate kinase2.7.4.80.442
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.442
2p83MR0Beta-secretase 13.4.23.460.442
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.442
3iktNADRedox-sensing transcriptional repressor Rex/0.442
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.442
3rdqDTBStreptavidin/0.442
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4u0mGTPCyclic GMP-AMP synthase/0.442
5dozNDPJamJ/0.442
1xp8AGSProtein RecA/0.441
2ibwCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.441
3ha5SFGHydroxymycolate synthase MmaA42.1.10.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3lpkZ76Beta-secretase 13.4.23.460.441
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.441
4k4fK4FTankyrase-12.4.2.300.441
4kbyC2EStimulator of interferon genes protein/0.441
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.441
4yfy1YJVioF/0.441
5dp2NAPCurF/0.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.440
1u1gBBBUridine phosphorylase2.4.2.30.440
1w0kADPATP synthase subunit alpha, mitochondrial/0.440
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.440
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2hm1LIQBeta-secretase 13.4.23.460.440
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.440
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.440
3drcMTXDihydrofolate reductase1.5.1.30.440
3l0lHC3Nuclear receptor ROR-gamma/0.440
3nmpPYVAbscisic acid receptor PYL2/0.440
3skgPB8Beta-secretase 13.4.23.460.440
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.440