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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
3n33AESBeta-peptidyl aminopeptidase BapA

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3n33AESBeta-peptidyl aminopeptidase BapA/1.000
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.524
2cleF6FTryptophan synthase alpha chain/0.486
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.482
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.480
3i0pNADMalate dehydrogenase, putative/0.479
2y6fM9FIsopenicillin N synthase1.21.3.10.476
2vcmM11Isopenicillin N synthase1.21.3.10.473
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.472
4nh82LCHeat shock protein HSP 90-alpha/0.472
4wx2F6FTryptophan synthase alpha chain/0.471
4wx2F6FTryptophan synthase beta chain4.2.1.200.471
1uy6PU3Heat shock protein HSP 90-alpha/0.470
3q43D66M1 family aminopeptidase3.4.110.470
4k4eK4ETankyrase-12.4.2.300.470
2clfF6FTryptophan synthase alpha chain/0.469
2vbpVB1Isopenicillin N synthase1.21.3.10.469
3gc8B45Mitogen-activated protein kinase 112.7.11.240.469
1txtCAAHMG-CoA synthase/0.466
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.465
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.464
1u0wSTLChalcone synthase 22.3.1.740.464
1oc1ASVIsopenicillin N synthase1.21.3.10.463
2e0nSAHPrecorrin-2 C20-methyltransferase/0.463
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.463
3pqbVGPPutative oxidoreductase/0.463
4n3r2GUTankyrase-12.4.2.300.463
4r20AERCytochrome P450 family 17 polypeptide 2/0.463
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.462
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.461
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.461
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.461
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
4n4t2GVTankyrase-12.4.2.300.460
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
3k1wBFXRenin3.4.23.150.459
3s7a684Dihydrofolate reductase1.5.1.30.459
3emlZMAAdenosine receptor A2a/0.459
1pd9CO4Dihydrofolate reductase1.5.1.30.458
2fwyH64Heat shock protein HSP 90-alpha/0.458
3ndvAICBeta-peptidyl aminopeptidase BapA/0.458
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.457
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.457
3zkyWT4Isopenicillin N synthase1.21.3.10.457
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.457
4j6cSTRCytochrome P450 monooxygenase/0.457
4xoqF42Coenzyme F420:L-glutamate ligase/0.457
1uyePU9Heat shock protein HSP 90-alpha/0.456
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.456
3zoiM2WIsopenicillin N synthase1.21.3.10.456
4bb3KKAIsopenicillin N synthase1.21.3.10.456
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.456
3tdaPN0Cytochrome P450 2D6/0.455
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
1blzACVIsopenicillin N synthase1.21.3.10.453
1ppjANYCytochrome b/0.453
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.453
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.453
4y6gF6FTryptophan synthase alpha chain/0.453
2fzjDH3Dihydrofolate reductase1.5.1.30.452
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.452
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1qiqACCIsopenicillin N synthase1.21.3.10.451
2iviACWIsopenicillin N synthase1.21.3.10.451
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.451
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.451
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.451
1bk0ACVIsopenicillin N synthase1.21.3.10.450
1hb3SCVIsopenicillin N synthase1.21.3.10.450
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.450
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2ykjYKJHeat shock protein HSP 90-alpha/0.450
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3qm4PN0Cytochrome P450 2D6/0.450
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
5k2aZMAAdenosine receptor A2a/0.450
3uzcT4EAdenosine receptor A2a/0.450
1ezfIN0Squalene synthase2.5.1.210.449
1qv0CZHObelin/0.449
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
3oadLPORenin3.4.23.150.449
4fqsLYAThymidylate synthase ThyA/0.449
4jpg1OXPyruvate kinase PKM2.7.1.400.449
1olmVTQSEC14-like protein 2/0.448
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1uymPU3Heat shock protein HSP 90-beta/0.448
3q44D50M1 family aminopeptidase3.4.110.448
4bfxZVXPantothenate kinase2.7.1.330.448
4g1nNZTPyruvate kinase PKM2.7.1.400.448
1s3uTQDDihydrofolate reductase1.5.1.30.447
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
3g70A5TRenin3.4.23.150.447
3mnrSD1Heat shock protein HSP 90-alpha/0.447
5k2bZMAAdenosine receptor A2a/0.447
1upw444Oxysterols receptor LXR-beta/0.446
3jsuKA5Bifunctional dihydrofolate reductase-thymidylate synthase/0.446
4bfpSWYTankyrase-22.4.2.300.446
5jtbZMAAdenosine receptor A2a/0.446
2dr3ADPUPF0273 protein PH0284/0.445
2vqoTFGHistone deacetylase 43.5.1.980.445
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.445
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.445
5bp9SAHPutative methyltransferase protein/0.445
3qakUKAAdenosine receptor A2a/0.445
1drfFOLDihydrofolate reductase1.5.1.30.444
1q5dEPBEpothilone C/D epoxidase1.140.444
2po7CHDFerrochelatase, mitochondrial4.99.1.10.444
3ft8MOJHeat shock protein HSP 90-alpha/0.444
3jpuTY4Transcriptional activator protein LasR/0.444
1pr0NOSPurine nucleoside phosphorylase DeoD-type/0.443
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.443
1uy8PU5Heat shock protein HSP 90-alpha/0.443
1uyfPU1Heat shock protein HSP 90-alpha/0.443
3nhfVVVRibosyldihydronicotinamide dehydrogenase [quinone]/0.443
3v94WYQPhosphodiesterase/0.443
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.443
1kzjCB3Thymidylate synthase/0.442
1zdwFLVPrenyltransferase/0.442
1zgaHMKIsoflavone 4'-O-methyltransferase/0.442
2clhF19Tryptophan synthase alpha chain/0.442
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.442
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.442
3ctj320Hepatocyte growth factor receptor2.7.10.10.442
3fnlSHALactoperoxidase/0.442
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.441
1s7gNADNAD-dependent protein deacylase 2/0.441
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.441
1uydPU8Heat shock protein HSP 90-alpha/0.441
1zg32HIIsoflavone 4'-O-methyltransferase/0.441
2vbdV10Isopenicillin N synthase1.21.3.10.441
3g72A6TRenin3.4.23.150.441
4b2gV1NUncharacterized protein/0.441
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.440
1uhlMEIRetinoic acid receptor RXR-beta/0.440
3ha3SAHHydroxymycolate synthase MmaA42.1.10.440
3pm1ETHTH-type transcriptional regulator QacR/0.440
3qczANPDihydrofolate synthase/folylpolyglutamate synthase/0.440
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.440
4i9i1DYTankyrase-12.4.2.300.440