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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
2ek4SAHDiphthine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2ek4SAHDiphthine synthase/1.000
2e4nSAHDiphthine synthase/0.883
2el3SAHDiphthine synthase/0.880
2eldSAHDiphthine synthase/0.875
2pb6SAHDiphthine synthase/0.856
2huvSAHDiphthine synthase/0.828
2huxSAHDiphthine synthase/0.802
2pcgSAHDiphthine synthase/0.790
2e8rSAHDiphthine synthase/0.784
2pchSAHDiphthine synthase/0.784
2dv3SAHDiphthine synthase/0.763
2e8qSAHDiphthine synthase/0.761
2owgSAHDiphthine synthase/0.761
2en5SAHDiphthine synthase/0.759
2pcaSAHDiphthine synthase/0.755
2ek2SAHDiphthine synthase/0.754
2z6rSAHDiphthine synthase/0.748
2eh4SAHDiphthine synthase/0.747
2huqSAHDiphthine synthase/0.741
2e7rSAHDiphthine synthase/0.736
2e07SAHDiphthine synthase/0.733
2p9dSAHDiphthine synthase/0.729
2ek7SAHDiphthine synthase/0.728
2eleSAHDiphthine synthase/0.726
2emuSAHDiphthine synthase/0.717
2dxxSAHDiphthine synthase/0.713
2pb4SAHDiphthine synthase/0.709
2dsgSAHDiphthine synthase/0.707
2el0SAHDiphthine synthase/0.705
2e17SAHDiphthine synthase/0.701
2e16SAHDiphthine synthase/0.699
2emrSAHDiphthine synthase/0.698
1wngSAHDiphthine synthase/0.697
2ed5SAHDiphthine synthase/0.690
2owkSAHDiphthine synthase/0.690
2pb5SAHDiphthine synthase/0.684
2eh5SAHDiphthine synthase/0.683
2ehlSAHDiphthine synthase/0.681
2pckSAHDiphthine synthase/0.681
2hutSAHDiphthine synthase/0.680
2eh2SAHDiphthine synthase/0.678
1vceSAHDiphthine synthase/0.677
2dxwSAHDiphthine synthase/0.675
2p6lSAHDiphthine synthase/0.673
2pcmSAHDiphthine synthase/0.671
2e8sSAHDiphthine synthase/0.667
2dxvSAHDiphthine synthase/0.666
2ek3SAHDiphthine synthase/0.662
2dekSAHDiphthine synthase/0.659
2hr8SAHDiphthine synthase/0.659
2p6dSAHDiphthine synthase/0.659
2eniSAHDiphthine synthase/0.650
2e15SAHDiphthine synthase/0.648
2ekaSAHDiphthine synthase/0.645
2dv5SAHDiphthine synthase/0.641
2ejjSAHDiphthine synthase/0.639
2p6iSAHDiphthine synthase/0.638
2e08SAHDiphthine synthase/0.637
2p5cSAHDiphthine synthase/0.636
2ejkSAHDiphthine synthase/0.634
2pciSAHDiphthine synthase/0.633
2dv4SAHDiphthine synthase/0.631
2egbSAHDiphthine synthase/0.630
2eglSAHDiphthine synthase/0.628
2ed3SAHDiphthine synthase/0.627
2dv7SAHDiphthine synthase/0.620
2p5fSAHDiphthine synthase/0.618
2owvSAHDiphthine synthase/0.611
2e8hSAHDiphthine synthase/0.595
2dshSAHDiphthine synthase/0.591
2owfSAHDiphthine synthase/0.590
2owuSAHDiphthine synthase/0.588
2p2xSAHDiphthine synthase/0.586
2dsiSAHDiphthine synthase/0.581
2p6kSAHDiphthine synthase/0.572
2egsSAHDiphthine synthase/0.570
2ejzSAHDiphthine synthase/0.568
2eeqSAHDiphthine synthase/0.562
1w6hTITPlasmepsin-23.4.23.390.504
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.490
3l9hEMQKinesin-like protein KIF11/0.483
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.483
1g1aNADdTDP-glucose 4,6-dehydratase/0.478
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.476
3a3gDLZLumazine protein/0.475
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
4djhJDCKappa-type opioid receptor/0.474
2ifaFMNUncharacterized protein/0.473
2hfuMEVMevalonate kinase/0.471
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.470
2rhgIGPTryptophan synthase alpha chain/0.469
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.468
2g8yNADHydroxycarboxylate dehydrogenase B/0.467
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.467
4wriOKAOkadaic acid binding protein 2-alpha/0.467
1dhrNADDihydropteridine reductase1.5.1.340.466
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.466
4i1iNADMalate dehydrogenase/0.466
1f8fNADBenzyl alcohol dehydrogenase/0.465
2gz8F3FOrf1a polyprotein/0.465
3fwiCAMCamphor 5-monooxygenase1.14.15.10.465
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.463
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.463
1civNAPMalate dehydrogenase [NADP], chloroplastic1.1.1.820.462
1h8hATPATP synthase subunit alpha, mitochondrial/0.462
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.462
2iviACWIsopenicillin N synthase1.21.3.10.462
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
1me6IVSPlasmepsin-23.4.23.390.461
4ougLP5Peptidoglycan recognition protein 1/0.461
1beuIPLTryptophan synthase alpha chain/0.460
1orrNADCDP-paratose 2-epimerase/0.460
2vwqNAPGlucose 1-dehydrogenase/0.460
3fwjCAMCamphor 5-monooxygenase1.14.15.10.460
3phjDHKShikimate dehydrogenase (NADP(+))/0.460
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.459
1pjcNADAlanine dehydrogenase/0.459
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.459
3wrhCAMCamphor 5-monooxygenase1.14.15.10.459
3zkyWT4Isopenicillin N synthase1.21.3.10.459
1x1cSAHC-20 methyltransferase/0.458
3wv9FEGHmd co-occurring protein HcgE/0.458
4cp4CAMCamphor 5-monooxygenase1.14.15.10.458
1o76CAMCamphor 5-monooxygenase1.14.15.10.457
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.457
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.457
3ijoB4DGlutamate receptor 2/0.456
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.456
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.456
3otwCOAPhosphopantetheine adenylyltransferase/0.456
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4wudANPDNA gyrase subunit B/0.456
1t86CAMCamphor 5-monooxygenase1.14.15.10.455
2a5kAZPReplicase polyprotein 1ab3.4.220.455
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.455
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.455
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.455
4prvADPDNA gyrase subunit B/0.455
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.454
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.454
3nl6TPSUncharacterized protein/0.454
3w6hAZMCarbonic anhydrase 14.2.1.10.454
3zh8C58Protein kinase C iota type2.7.11.130.454
2gjlFMNNitronate monooxygenase1.13.12.160.453
2pswCOAN-alpha-acetyltransferase 50/0.453
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1dz4CAMCamphor 5-monooxygenase1.14.15.10.452
1yqzCOACoenzyme A disulfide reductase/0.452
1yrcCAMCamphor 5-monooxygenase1.14.15.10.452
3gqvNAPEnoyl reductase LovC10.452
3px3T3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.452
4gg1TZDBenzoylformate decarboxylase4.1.1.70.452
1jedADPSulfate adenylyltransferase/0.451
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.451
2x7hPFNProstaglandin reductase 310.451
3lxiCAMCytochrome P450/0.451
3t3r9PLCytochrome P450 2A61.14.130.451
4a83DXCMajor pollen allergen Bet v 1-A/0.451
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1drhNAPDihydrofolate reductase1.5.1.30.450
1t2cNAIL-lactate dehydrogenase1.1.1.270.450
1yrdCAMCamphor 5-monooxygenase1.14.15.10.450
2a94AP0L-lactate dehydrogenase1.1.1.270.450
2q4bNAPUncharacterized protein At5g02240/0.450
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.450
2y0mACOHistone acetyltransferase KAT8/0.450
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3ig6438Urokinase-type plasminogen activator3.4.21.730.450
3sf6FDAGlutaryl-CoA dehydrogenase/0.450
3vt7VDXVitamin D3 receptor/0.450
1f20FADNitric oxide synthase, brain1.14.13.390.449
1nooCAHCamphor 5-monooxygenase1.14.15.10.449
1xzqFONtRNA modification GTPase MnmE3.6.50.449
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.449
2gjnFMNNitronate monooxygenase1.13.12.160.449
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.449
3fwgCAMCamphor 5-monooxygenase1.14.15.10.449
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.449
4f5yC2EStimulator of interferon genes protein/0.449
1dr2TAPDihydrofolate reductase1.5.1.30.448
1ia1NDPDihydrofolate reductase1.5.1.30.448
1ohhANPATP synthase subunit alpha, mitochondrial/0.448
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.448
1udaUFGUDP-glucose 4-epimerase5.1.3.20.448
2a1mCAMCamphor 5-monooxygenase1.14.15.10.448
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.448
2w3bNDPDihydrofolate reductase1.5.1.30.448
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.448
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.448
4ek1CAMCamphor 5-monooxygenase1.14.15.10.448
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4l4cCAMCamphor 5-monooxygenase1.14.15.10.448
4q71FADBifunctional protein PutA/0.448
1npvL27Gag-Pol polyprotein3.4.23.160.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
2vkeTACTetracycline repressor protein class D/0.447
2ylzFADPhenylacetone monooxygenase1.14.13.920.447
3fznD7KBenzoylformate decarboxylase4.1.1.70.447
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.447
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.447
4eji0QACytochrome P450 2A131.14.14.10.447
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.447
4opgFDAConserved Archaeal protein/0.447
1juvNDPDihydrofolate reductase1.5.1.30.446
2e0nSAHPrecorrin-2 C20-methyltransferase/0.446
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.446
2v7qATPATP synthase subunit alpha, mitochondrial/0.446
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.446
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
1qoqIGPTryptophan synthase alpha chain/0.445
1t88CAMCamphor 5-monooxygenase1.14.15.10.445
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.445
1xl5190Gag-Pol polyprotein3.4.23.160.445
2he5NDPAldo-keto reductase family 1 member C211.1.10.445
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
2xhd7T9Glutamate receptor 2/0.445
2y3sTIRTamL/0.445
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.445
3orfNADDihydropteridine reductase1.5.1.340.445
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.445
3wrjCAMCamphor 5-monooxygenase1.14.15.10.445
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.445
5dp2NAPCurF/0.445
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1re7FOLDihydrofolate reductase1.5.1.30.444
2a9y26AAdenosine kinase2.7.1.200.444
2wo7ASVIsopenicillin N synthase1.21.3.10.444
3aezGDPPantothenate kinase2.7.1.330.444
3in6FMNUncharacterized protein/0.444
3q43D66M1 family aminopeptidase3.4.110.444
4ejgNCTCytochrome P450 2A131.14.14.10.444
4gsuDWZL,D-transpeptidase 22.3.20.444
4oztP1AEcdysone receptor, putative/0.444
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.443
1tqf32PBeta-secretase 13.4.23.460.443
2g1n1IGRenin3.4.23.150.443
2iyfERYOleandomycin glycosyltransferase2.4.10.443
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.443
2qbmCAMCamphor 5-monooxygenase1.14.15.10.443
3h3t16HCollagen type IV alpha-3-binding protein/0.443
3hl0NADMaleylacetate reductase/0.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
3wrlCAMCamphor 5-monooxygenase1.14.15.10.443
4ipw1G7Mycocyclosin synthase1.14.21.90.443
1bdlIM1Gag-Pol polyprotein3.4.23.160.442
1mj9COAHistone acetyltransferase ESA1/0.442
1o97FADElectron transfer flavoprotein subunit alpha/0.442
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.442
1u3dFADCryptochrome-1/0.442
2b8l5HABeta-secretase 13.4.23.460.442
2c20NADUDP-glucose 4-epimerase/0.442
2p5uNADUDP-glucose 4-epimerase/0.442
2qimZEAClass 10 plant pathogenesis-related protein/0.442
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.442
3clrFADElectron transfer flavoprotein subunit alpha/0.442
3zoiM2WIsopenicillin N synthase1.21.3.10.442
4twnB96Ephrin type-A receptor 32.7.10.10.442
1ptjSNDNAD(P) transhydrogenase subunit alpha part 11.6.1.20.441
1u2rSO1Elongation factor 2/0.441
1uyuCAMCamphor 5-monooxygenase1.14.15.10.441
1xe55FEPlasmepsin-23.4.23.390.441
2p3b3TLV-1 PROTEASE protein/0.441
2p3b3TLV-1 protease/0.441
2rcyNAPPyrroline-5-carboxylate reductase/0.441
2rh9IGPTryptophan synthase alpha chain/0.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3em3478Gag-Pol polyprotein3.4.23.160.441
3lqfNADGalactitol dehydrogenase/0.441
4dzzADPPlasmid partitioning protein ParF/0.441
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.441
4ktkKTKCytochrome P450/0.441
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.441
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.440
1k7fIAVTryptophan synthase alpha chain/0.440
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.440
2givACOHistone acetyltransferase KAT8/0.440
4fhd0TTSpore photoproduct lyase/0.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440