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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
2d81RB3Poly(3-hydroxybutyrate) depolymerase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2d81RB3Poly(3-hydroxybutyrate) depolymerase/1.000
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.486
2xlrFADPutative flavin-containing monooxygenase/0.478
1xddAAYIntegrin alpha-L/0.477
1w6hTITPlasmepsin-23.4.23.390.476
4q0kGA3Phytohormone-binding protein/0.476
2fznFADBifunctional protein PutA1.5.5.20.474
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.474
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.473
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.472
4g7gVFVLanosterol 14-alpha-demethylase/0.471
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.470
5irnADPNucleotide binding oligomerization domain containing 2/0.470
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.467
3tfyCOAN-alpha-acetyltransferase 502.3.10.467
3ekuCY9Actin-5C/0.466
3h3qH13Collagen type IV alpha-3-binding protein/0.466
2xfsJ01Uncharacterized protein/0.465
2xgoZKDUncharacterized protein/0.465
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.464
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.464
1q23FUAChloramphenicol acetyltransferase2.3.1.280.462
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.462
1fm4DXCMajor pollen allergen Bet v 1-L/0.461
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.461
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
2flhZEACytokinin-specific binding protein/0.460
3af1GDPPantothenate kinase2.7.1.330.460
3s1dZIRCytokinin dehydrogenase 11.5.99.120.460
2fhnBNIAvidin-related protein 4/5/0.459
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.459
4a84DXCMajor pollen allergen Bet v 1-A/0.459
4fm80UQBeta-secretase 13.4.23.460.459
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.458
2gv8NDPThiol-specific monooxygenase1.14.130.458
4ambDUDPutative glycosyl transferase/0.458
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.458
1me6IVSPlasmepsin-23.4.23.390.457
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.457
4l5b1UXDeoxycytidine kinase2.7.1.740.457
1fmlRTLRetinol dehydratase/0.456
2iviACWIsopenicillin N synthase1.21.3.10.456
3to3ATPPetrobactin biosynthesis protein AsbB/0.456
1bk0ACVIsopenicillin N synthase1.21.3.10.455
2ifaFMNUncharacterized protein/0.455
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.454
1tj1FADBifunctional protein PutA1.5.5.20.454
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.454
4eb5PLPCysteine desulfurase IscS 2/0.454
3jpuTY4Transcriptional activator protein LasR/0.453
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.453
4q73FADBifunctional protein PutA/0.453
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.453
4bb3KKAIsopenicillin N synthase1.21.3.10.452
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.452
4eqwCOACoenzyme A disulfide reductase/0.451
1hb3SCVIsopenicillin N synthase1.21.3.10.450
2g1r3IGRenin3.4.23.150.450
2igoFADPyranose 2-oxidase/0.450
2jb4A14Isopenicillin N synthase1.21.3.10.450
2prbCOAAminoglycoside 6-N-acetyltransferase type Ib11/0.450
2zbaZBATrichothecene 3-O-acetyltransferase/0.450
3d91REMRenin3.4.23.150.450
3ru9NADUDP-N-acetylglucosamine 4-epimerase/0.450
4bfuZVUPantothenate kinase2.7.1.330.450
4eb7PLPCysteine desulfurase IscS 2/0.450
4jlm1NNDeoxycytidine kinase2.7.1.740.450
1yqzCOACoenzyme A disulfide reductase/0.449
2gjlFMNNitronate monooxygenase1.13.12.160.449
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.449
2v59LZKBiotin carboxylase6.3.4.140.449
2xgs44PUncharacterized protein/0.449
3gfbNADL-threonine 3-dehydrogenase/0.449
4psbGA3Cytokinin-specific binding protein/0.449
1udaUFGUDP-glucose 4-epimerase5.1.3.20.448
2g8yNADHydroxycarboxylate dehydrogenase B/0.448
2ie0ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.448
4a83DXCMajor pollen allergen Bet v 1-A/0.448
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.448
4k6fNAPPutative Acetoacetyl-CoA reductase/0.448
4yryFADGlutamate synthase, beta subunit/0.448
1c7oPPGHemolysin/0.447
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1xe65FPPlasmepsin-23.4.23.390.447
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
2fzmFADBifunctional protein PutA1.5.5.20.447
2il2LIXRenin3.4.23.150.447
3ix8TX3Transcriptional activator protein LasR/0.447
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.447
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.447
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.447
4egbNADdTDP-glucose 4,6-dehydratase/0.447
4gl4NAIAlcohol dehydrogenase class-3/0.447
4uyf73BBromodomain-containing protein 2/0.447
1lnmDTXBilin-binding protein/0.446
1x1bSAHC-20 methyltransferase/0.446
2ftoCB3Thymidylate synthase/0.446
2rehFADNitroalkane oxidase1.7.3.10.446
3fktSIIBeta-secretase 13.4.23.460.446
3h3r14HCollagen type IV alpha-3-binding protein/0.446
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.446
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.446
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
4araC56Acetylcholinesterase3.1.1.70.446
4g3jVNTLanosterol 14-alpha-demethylase/0.446
1ay0TPPTransketolase 12.2.1.10.445
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
2f3fAXFBeta-secretase 13.4.23.460.445
2ignFADPyranose 2-oxidase/0.445
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.445
3h3t16HCollagen type IV alpha-3-binding protein/0.445
3phiNDPShikimate dehydrogenase (NADP(+))/0.445
4frkDWDBeta-secretase 13.4.23.460.445
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
2ejvNADL-threonine 3-dehydrogenase/0.444
2uzfCAA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.444
3af0GDPPantothenate kinase2.7.1.330.444
4a81DXCMajor pollen allergen Bet v 1-A/0.444
4df2FMNNADPH dehydrogenase/0.444
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.444
1pq944BOxysterols receptor LXR-beta/0.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
1z7yAA5Cysteine synthase 12.5.1.470.443
2p4j23IBeta-secretase 13.4.23.460.443
3gf4UPGUDP-galactopyranose mutase5.4.99.90.443
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4kgmATPUncharacterized protein/0.443
1t2cNAIL-lactate dehydrogenase1.1.1.270.442
1tj2FADBifunctional protein PutA1.5.5.20.442
1xs7MMIBeta-secretase 13.4.23.460.442
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.442
2po7CHDFerrochelatase, mitochondrial4.99.1.10.442
2xlsFADPutative flavin-containing monooxygenase/0.442
3afhGSUGlutamate--tRNA ligase 2/0.442
3djjFADGlutathione reductase, mitochondrial1.8.1.70.442
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.442
4ejmNAPPutative zinc-binding dehydrogenase/0.442
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.441
2r96FMNNAD(P)H dehydrogenase (quinone)/0.441
2whqHI6Acetylcholinesterase3.1.1.70.441
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3ibdCPZCytochrome P450 2B61.14.130.441
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.441
4a6rTA8Probable aminotransferase/0.441
4b66NAPL-ornithine N(5)-monooxygenase/0.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4q71FADBifunctional protein PutA/0.441
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
5dp2NAPCurF/0.441
1icsFMN12-oxophytodienoate reductase 11.3.1.420.440
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.440
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.440
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3nsh957Beta-secretase 13.4.23.460.440
3oqfS51Renin3.4.23.150.440
4dc0NDPPutative ketoacyl reductase1.3.10.440
4i0i957Beta-secretase 13.4.23.460.440
4nbwNADShort-chain dehydrogenase/reductase SDR/0.440
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.440