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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
2pcmSAHDiphthine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2pcmSAHDiphthine synthase/1.000
2emrSAHDiphthine synthase/0.898
2eh5SAHDiphthine synthase/0.864
2dxvSAHDiphthine synthase/0.858
2dxwSAHDiphthine synthase/0.847
2ek7SAHDiphthine synthase/0.835
2e8qSAHDiphthine synthase/0.834
2p6dSAHDiphthine synthase/0.828
2eniSAHDiphthine synthase/0.815
2e8sSAHDiphthine synthase/0.813
2emuSAHDiphthine synthase/0.813
2ehlSAHDiphthine synthase/0.803
2dv7SAHDiphthine synthase/0.801
2pb4SAHDiphthine synthase/0.800
2ekaSAHDiphthine synthase/0.794
2eglSAHDiphthine synthase/0.791
2ejkSAHDiphthine synthase/0.788
2en5SAHDiphthine synthase/0.787
2dsgSAHDiphthine synthase/0.775
2e16SAHDiphthine synthase/0.761
2huxSAHDiphthine synthase/0.757
2owkSAHDiphthine synthase/0.755
2eleSAHDiphthine synthase/0.747
2el0SAHDiphthine synthase/0.743
2egsSAHDiphthine synthase/0.737
2ed5SAHDiphthine synthase/0.723
2pb6SAHDiphthine synthase/0.721
2dv4SAHDiphthine synthase/0.713
2eh2SAHDiphthine synthase/0.711
2pcgSAHDiphthine synthase/0.710
2p6kSAHDiphthine synthase/0.709
2e7rSAHDiphthine synthase/0.707
2dv3SAHDiphthine synthase/0.701
2egbSAHDiphthine synthase/0.696
2p2xSAHDiphthine synthase/0.691
1wngSAHDiphthine synthase/0.687
2pchSAHDiphthine synthase/0.680
2p5cSAHDiphthine synthase/0.679
2owvSAHDiphthine synthase/0.672
2ek2SAHDiphthine synthase/0.671
2hutSAHDiphthine synthase/0.670
2dxxSAHDiphthine synthase/0.666
2p5fSAHDiphthine synthase/0.664
2dekSAHDiphthine synthase/0.661
1vceSAHDiphthine synthase/0.657
2hr8SAHDiphthine synthase/0.656
2ek4SAHDiphthine synthase/0.654
2e8rSAHDiphthine synthase/0.652
2e8hSAHDiphthine synthase/0.650
2pcaSAHDiphthine synthase/0.650
2e08SAHDiphthine synthase/0.645
2pckSAHDiphthine synthase/0.645
2eldSAHDiphthine synthase/0.642
2ek3SAHDiphthine synthase/0.640
2p6iSAHDiphthine synthase/0.635
2e4nSAHDiphthine synthase/0.634
2p6lSAHDiphthine synthase/0.630
2huvSAHDiphthine synthase/0.629
2dsiSAHDiphthine synthase/0.628
2pciSAHDiphthine synthase/0.626
2el3SAHDiphthine synthase/0.623
2eh4SAHDiphthine synthase/0.614
2p9dSAHDiphthine synthase/0.612
2z6rSAHDiphthine synthase/0.612
2e17SAHDiphthine synthase/0.606
2owgSAHDiphthine synthase/0.604
2e15SAHDiphthine synthase/0.600
2dv5SAHDiphthine synthase/0.598
2eeqSAHDiphthine synthase/0.589
2e07SAHDiphthine synthase/0.572
2owfSAHDiphthine synthase/0.569
2ejjSAHDiphthine synthase/0.567
2owuSAHDiphthine synthase/0.567
2huqSAHDiphthine synthase/0.551
2ejzSAHDiphthine synthase/0.545
2dshSAHDiphthine synthase/0.530
2ed3SAHDiphthine synthase/0.520
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.487
1xe55FEPlasmepsin-23.4.23.390.483
1lbcCYZGlutamate receptor 2/0.481
1e1qANPATP synthase subunit alpha, mitochondrial/0.480
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.480
1h8hATPATP synthase subunit alpha, mitochondrial/0.477
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.477
2gjlFMNNitronate monooxygenase1.13.12.160.473
1g63FMNEpidermin decarboxylase4.1.10.470
3b70NAPEnoyl reductase LovC10.469
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.469
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
4i1iNADMalate dehydrogenase/0.467
4ougLP5Peptidoglycan recognition protein 1/0.467
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.465
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.464
4f5yC2EStimulator of interferon genes protein/0.463
1bmfANPATP synthase subunit alpha, mitochondrial/0.461
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.461
2cy0NAPShikimate dehydrogenase (NADP(+))/0.461
2q5g1FAPeroxisome proliferator-activated receptor delta/0.461
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
2gjnFMNNitronate monooxygenase1.13.12.160.460
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.460
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
4la1FADThioredoxin glutathione reductase/0.459
1nvtNAPShikimate dehydrogenase (NADP(+))/0.458
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.458
3a3gDLZLumazine protein/0.458
4g3jVNTLanosterol 14-alpha-demethylase/0.458
3w6hAZMCarbonic anhydrase 14.2.1.10.457
3zh8C58Protein kinase C iota type2.7.11.130.457
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.457
1udaUFGUDP-glucose 4-epimerase5.1.3.20.456
2gz8F3FOrf1a polyprotein/0.456
3ik6HCZGlutamate receptor 2/0.456
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.456
2e0nSAHPrecorrin-2 C20-methyltransferase/0.455
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.455
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.455
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.455
5d3qGDPDynamin-13.6.5.50.455
2a94AP0L-lactate dehydrogenase1.1.1.270.454
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.454
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.453
1xe65FPPlasmepsin-23.4.23.390.453
2qbuSAHPrecorrin-2 methyltransferase/0.453
2vwqNAPGlucose 1-dehydrogenase/0.453
3s1dZIRCytokinin dehydrogenase 11.5.99.120.453
4wudANPDNA gyrase subunit B/0.453
1dyiFOLDihydrofolate reductase1.5.1.30.452
3in6FMNUncharacterized protein/0.452
3vqsJT1Genome polyprotein/0.452
1ddsMTXDihydrofolate reductase1.5.1.30.451
1dr3HBIDihydrofolate reductase1.5.1.30.451
1o9bNAIQuinate/shikimate dehydrogenase/0.451
1xddAAYIntegrin alpha-L/0.451
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.451
3d91REMRenin3.4.23.150.451
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.451
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.451
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.451
1bxoPP7Penicillopepsin-13.4.23.200.450
1cf3FADGlucose oxidase1.1.3.40.450
1fxsNAPGDP-L-fucose synthase/0.450
1re7FOLDihydrofolate reductase1.5.1.30.450
2g8yNADHydroxycarboxylate dehydrogenase B/0.450
2pj4414Carboxypeptidase B/0.450
2wedPP6Penicillopepsin-13.4.23.200.450
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.450
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3ig6438Urokinase-type plasminogen activator3.4.21.730.450
3tjzGNPADP-ribosylation factor 1/0.450
1bdlIM1Gag-Pol polyprotein3.4.23.160.449
1f20FADNitric oxide synthase, brain1.14.13.390.449
1xl5190Gag-Pol polyprotein3.4.23.160.449
2f1kNAPPrephenate dehydrogenase/0.449
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3vt7VDXVitamin D3 receptor/0.449
4dbzNDPPutative ketoacyl reductase1.3.10.449
4m4922YL-lactate dehydrogenase A chain1.1.1.270.449
4djhJDCKappa-type opioid receptor/0.449
1bim0QBRenin3.4.23.150.448
1dhjMTXDihydrofolate reductase1.5.1.30.448
1e7qNAPGDP-L-fucose synthase/0.448
2p33J07Mitogen-activated protein kinase 102.7.11.240.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.448
1drhNAPDihydrofolate reductase1.5.1.30.447
1hzjUD1UDP-glucose 4-epimerase/0.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
2hxzH7JCathepsin S3.4.22.270.447
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.447
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.447
3t4eNADQuinate/shikimate dehydrogenase/0.447
4ipw1G7Mycocyclosin synthase1.14.21.90.447
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.446
2znnS44Peroxisome proliferator-activated receptor alpha/0.446
2zvcSAHPrecorrin-3 C17-methyltransferase/0.446
3orfNADDihydropteridine reductase1.5.1.340.446
3tneRITCandidapepsin-13.4.23.240.446
4g47TZFMycocyclosin synthase1.14.21.90.446
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.446
4h1e10JBeta-secretase 13.4.23.460.446
4h3f10OBeta-secretase 13.4.23.460.446
1tqf32PBeta-secretase 13.4.23.460.445
1v35NAIEnoyl-ACP reductase/0.445
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3lpkZ76Beta-secretase 13.4.23.460.445
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.445
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.445
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.445
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.445
1vikBAYGag-Pol polyprotein/0.444
2pswCOAN-alpha-acetyltransferase 50/0.444
2y3sTIRTamL/0.444
2yj4ATPCopper-transporting ATPase/0.444
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3gqvNAPEnoyl reductase LovC10.444
4a5lFADThioredoxin reductase/0.444
4j0v1H7Beta-secretase 13.4.23.460.444
4prvADPDNA gyrase subunit B/0.444
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1bwsNDPGDP-L-fucose synthase/0.443
1dirNADDihydropteridine reductase1.5.1.340.443
1yqzCOACoenzyme A disulfide reductase/0.443
2rh9IGPTryptophan synthase alpha chain/0.443
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.443
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.443
3v0p4GWHisto-blood group ABO system transferase/0.443
4b70WM9Beta-secretase 13.4.23.460.443
4ejgNCTCytochrome P450 2A131.14.14.10.443
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.442
1f8fNADBenzyl alcohol dehydrogenase/0.442
1kfcIPLTryptophan synthase alpha chain/0.442
1qoqIGPTryptophan synthase alpha chain/0.442
1rkwPNTHTH-type transcriptional regulator QacR/0.442
2c20NADUDP-glucose 4-epimerase/0.442
2g1s4IGRenin3.4.23.150.442
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.442
2p5uNADUDP-glucose 4-epimerase/0.442
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3p0hFSEPutative tyrosyl-tRNA synthetase/0.442
4cp4CAMCamphor 5-monooxygenase1.14.15.10.442
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.441
1nzdUPGDNA beta-glucosyltransferase/0.441
2cftPLPPyridoxal phosphate phosphatase/0.441
2hfuMEVMevalonate kinase/0.441
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.441
2rcyNAPPyrroline-5-carboxylate reductase/0.441
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
3nr4PYVAbscisic acid receptor PYL2/0.441
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.441
4ejh0QACytochrome P450 2A131.14.14.10.441
4ejmNAPPutative zinc-binding dehydrogenase/0.441
4kkyCAMCamphor 5-monooxygenase1.14.15.10.441
4m83ERYOleandomycin glycosyltransferase2.4.10.441
4nvk2NYPeroxidase/0.441
4q71FADBifunctional protein PutA/0.441
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.441
1bil0IURenin3.4.23.150.440
1k8y13PTryptophan synthase alpha chain/0.440
2d29FADAcyl-CoA dehydrogenase/0.440
2q0lNAPThioredoxin reductase1.8.1.90.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.440
3q43D66M1 family aminopeptidase3.4.110.440
3slkNDPPolyketide synthase extender module 2/0.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4dh60KNBeta-secretase 13.4.23.460.440
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.440
4g2gTDHMycocyclosin synthase1.14.21.90.440
4j75TYMTryptophan--tRNA ligase/0.440
4tuvCPZCytochrome P450 1191.140.440
4v2gITCTetracycline repressor protein class D/0.440
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.440