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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.11.000
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.11.000
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.786
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.786
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.651
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.651
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.630
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.622
3m2rCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.589
3m2rCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.589
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.475
3u9eCOALmo1369 protein/0.474
4i6gFADCryptochrome-2/0.470
2eixFADNADH-cytochrome b5 reductase/0.469
3muoZPRProlyl endopeptidase/0.466
1uxyEPUUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.465
3eo8FMNPutative nitroreductase/0.463
3lpiZ74Beta-secretase 13.4.23.460.462
2g1s4IGRenin3.4.23.150.460
2g1y5IGRenin3.4.23.150.460
3tr05GPGuanylate kinase/0.460
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.458
1xe65FPPlasmepsin-23.4.23.390.457
2a94AP0L-lactate dehydrogenase1.1.1.270.456
4bfwZVWPantothenate kinase2.7.1.330.456
1gtrATPGlutamine--tRNA ligase6.1.1.180.455
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.454
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.453
1ooqFMNOxygen-insensitive NAD(P)H nitroreductase/0.453
2g247IGRenin3.4.23.150.453
1l7x700Glycogen phosphorylase, liver form2.4.1.10.452
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.452
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.451
4bfzZVZPantothenate kinase2.7.1.330.451
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.450
3qgf46FGenome polyprotein2.7.7.480.450
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.449
2gjnFMNNitronate monooxygenase1.13.12.160.449
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.448
2xfyACXBeta-amylase3.2.1.20.448
3k6l2BBPeptide deformylase3.5.1.880.448
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.448
2g1r3IGRenin3.4.23.150.447
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.447
2r7pANPNon-structural protein 23.6.40.447
4ef9FMNDihydroorotate dehydrogenase (fumarate)/0.447
4ipw1G7Mycocyclosin synthase1.14.21.90.447
4tmbFMNOld yellow enzyme/0.447
4ycoFMNtRNA-dihydrouridine(16) synthase/0.447
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.446
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.445
2xuhTZ4Acetylcholinesterase3.1.1.70.445
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.445
3uayADNPurine nucleoside phosphorylase DeoD-type/0.445
1udaUFGUDP-glucose 4-epimerase5.1.3.20.444
1xe55FEPlasmepsin-23.4.23.390.444
2rc3NADCBS domain/0.444
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.444
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.444
1fyfSSAThreonine--tRNA ligase6.1.1.30.443
1xvaSAMGlycine N-methyltransferase2.1.1.200.443
2b53D23Cyclin-dependent kinase 22.7.11.220.443
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.443
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.443
4egbNADdTDP-glucose 4,6-dehydratase/0.443
4loi1YCStimulator of interferon genes protein/0.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
1nzdUPGDNA beta-glucosyltransferase/0.442
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.442
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.442
2oapANPType II secretion system protein (GspE-2)/0.442
4ke11R6Beta-secretase 13.4.23.460.442
4y7cFADNADPH--cytochrome P450 reductase/0.442
1p0ySAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.441
2cftPLPPyridoxal phosphate phosphatase/0.441
2ft9CHDFatty acid-binding protein 2, liver/0.440
2hk9NAPShikimate dehydrogenase (NADP(+))/0.440
3pm1ETHTH-type transcriptional regulator QacR/0.440