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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
2dv3SAHDiphthine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2dv3SAHDiphthine synthase/1.000
2pchSAHDiphthine synthase/0.814
2e8qSAHDiphthine synthase/0.802
1wngSAHDiphthine synthase/0.792
2dxxSAHDiphthine synthase/0.785
2pcaSAHDiphthine synthase/0.779
2eldSAHDiphthine synthase/0.776
2p9dSAHDiphthine synthase/0.775
2eh4SAHDiphthine synthase/0.773
2huxSAHDiphthine synthase/0.771
2pcgSAHDiphthine synthase/0.758
2el0SAHDiphthine synthase/0.757
2e7rSAHDiphthine synthase/0.752
2ek7SAHDiphthine synthase/0.746
2el3SAHDiphthine synthase/0.744
2en5SAHDiphthine synthase/0.742
2owgSAHDiphthine synthase/0.741
2pb4SAHDiphthine synthase/0.736
2pb6SAHDiphthine synthase/0.735
2e4nSAHDiphthine synthase/0.733
2huqSAHDiphthine synthase/0.728
2huvSAHDiphthine synthase/0.727
2pckSAHDiphthine synthase/0.727
2dsgSAHDiphthine synthase/0.724
2pb5SAHDiphthine synthase/0.724
2dv7SAHDiphthine synthase/0.714
2ejjSAHDiphthine synthase/0.713
2dv4SAHDiphthine synthase/0.712
2dxvSAHDiphthine synthase/0.712
2dxwSAHDiphthine synthase/0.712
2ek4SAHDiphthine synthase/0.708
2p6iSAHDiphthine synthase/0.705
2e07SAHDiphthine synthase/0.698
2p6lSAHDiphthine synthase/0.691
2emrSAHDiphthine synthase/0.687
2dshSAHDiphthine synthase/0.685
2e8sSAHDiphthine synthase/0.685
2eh5SAHDiphthine synthase/0.685
2p5cSAHDiphthine synthase/0.683
2pcmSAHDiphthine synthase/0.682
2emuSAHDiphthine synthase/0.677
2ejkSAHDiphthine synthase/0.670
2eniSAHDiphthine synthase/0.670
2ed5SAHDiphthine synthase/0.669
1vceSAHDiphthine synthase/0.665
2e08SAHDiphthine synthase/0.661
2dekSAHDiphthine synthase/0.660
2eleSAHDiphthine synthase/0.658
2z6rSAHDiphthine synthase/0.655
2ek2SAHDiphthine synthase/0.652
2e8hSAHDiphthine synthase/0.651
2e16SAHDiphthine synthase/0.649
2egbSAHDiphthine synthase/0.647
2ekaSAHDiphthine synthase/0.645
2e8rSAHDiphthine synthase/0.644
2ehlSAHDiphthine synthase/0.642
2eglSAHDiphthine synthase/0.641
2p6dSAHDiphthine synthase/0.641
2dv5SAHDiphthine synthase/0.640
2hr8SAHDiphthine synthase/0.638
2pciSAHDiphthine synthase/0.635
2p5fSAHDiphthine synthase/0.628
2egsSAHDiphthine synthase/0.625
2ek3SAHDiphthine synthase/0.624
2ed3SAHDiphthine synthase/0.619
2owvSAHDiphthine synthase/0.619
2dsiSAHDiphthine synthase/0.603
2hutSAHDiphthine synthase/0.602
2eeqSAHDiphthine synthase/0.594
2owuSAHDiphthine synthase/0.593
2e17SAHDiphthine synthase/0.592
2p2xSAHDiphthine synthase/0.591
2p6kSAHDiphthine synthase/0.590
2eh2SAHDiphthine synthase/0.584
2owkSAHDiphthine synthase/0.573
2e15SAHDiphthine synthase/0.569
2owfSAHDiphthine synthase/0.567
2ejzSAHDiphthine synthase/0.520
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.490
1xe55FEPlasmepsin-23.4.23.390.470
1f8fNADBenzyl alcohol dehydrogenase/0.464
1w6hTITPlasmepsin-23.4.23.390.461
3vt7VDXVitamin D3 receptor/0.461
4ougLP5Peptidoglycan recognition protein 1/0.461
2givACOHistone acetyltransferase KAT8/0.460
2a94AP0L-lactate dehydrogenase1.1.1.270.458
2g8yNADHydroxycarboxylate dehydrogenase B/0.458
3wv9FEGHmd co-occurring protein HcgE/0.456
2gjlFMNNitronate monooxygenase1.13.12.160.455
3b70NAPEnoyl reductase LovC10.452
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.452
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4bfzZVZPantothenate kinase2.7.1.330.451
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.450
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.450
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.450
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.450
1rneC60Renin3.4.23.150.449
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
1k8y13PTryptophan synthase alpha chain/0.448
4bfxZVXPantothenate kinase2.7.1.330.448
1qoqIGPTryptophan synthase alpha chain/0.447
2znnS44Peroxisome proliferator-activated receptor alpha/0.447
3p62FMNPentaerythritol tetranitrate reductase/0.447
3slkNDPPolyketide synthase extender module 2/0.447
5dp2NAPCurF/0.447
1ddrMTXDihydrofolate reductase1.5.1.30.446
2q4bNAPUncharacterized protein At5g02240/0.446
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.445
2npaMMBPeroxisome proliferator-activated receptor alpha/0.445
2rhgIGPTryptophan synthase alpha chain/0.445
3l9hEMQKinesin-like protein KIF11/0.445
1xddAAYIntegrin alpha-L/0.444
3djjFADGlutathione reductase, mitochondrial1.8.1.70.444
3ijoB4DGlutamate receptor 2/0.444
3w6hAZMCarbonic anhydrase 14.2.1.10.444
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1xe65FPPlasmepsin-23.4.23.390.442
2e0nSAHPrecorrin-2 C20-methyltransferase/0.442
2ifaFMNUncharacterized protein/0.442
3mjrAC2Deoxycytidine kinase2.7.1.740.442
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
1tqf32PBeta-secretase 13.4.23.460.441
1udaUFGUDP-glucose 4-epimerase5.1.3.20.441
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.441
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
1kkq471Peroxisome proliferator-activated receptor alpha/0.440
1o76CAMCamphor 5-monooxygenase1.14.15.10.440
2gz8F3FOrf1a polyprotein/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fznD7KBenzoylformate decarboxylase4.1.1.70.440
3vt9YI4Vitamin D3 receptor/0.440
4g3jVNTLanosterol 14-alpha-demethylase/0.440