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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
4bvhOCZNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4bvhOCZNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.11.000
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.516
3cr0809Wee1-like protein kinase2.7.10.20.483
4pabTHGDimethylglycine dehydrogenase, mitochondrial1.5.8.40.483
3biz61EWee1-like protein kinase2.7.10.20.481
1s7gNADNAD-dependent protein deacylase 2/0.479
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.478
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.470
1fmlRTLRetinol dehydratase/0.469
1pqc444Oxysterols receptor LXR-beta/0.467
1x8lOXRRetinol dehydratase/0.467
1pd9CO4Dihydrofolate reductase1.5.1.30.466
1q23FUAChloramphenicol acetyltransferase2.3.1.280.466
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.466
4j6dTESCytochrome P450 monooxygenase/0.466
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.464
2getCOKPantothenate kinase2.7.1.330.464
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.464
4rh10TTSpore photoproduct lyase/0.464
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.464
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.463
1yc2NADNAD-dependent protein deacylase 2/0.461
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.460
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.460
3nt5NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.459
3v94WYQPhosphodiesterase/0.459
1g63FMNEpidermin decarboxylase4.1.10.458
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.458
5dp2NAPCurF/0.457
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.456
2ejzSAHDiphthine synthase/0.456
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.456
3uyk0CXProbable NDP-rhamnosyltransferase/0.455
1s3uTQDDihydrofolate reductase1.5.1.30.454
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.454
2z2w770Wee1-like protein kinase2.7.10.20.454
3irxUDRGag-Pol polyprotein2.7.7.490.454
4b2gV1NUncharacterized protein/0.454
2in6839Wee1-like protein kinase2.7.10.20.453
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
3ihgVAKAklavinone 12-hydroxylase RdmE/0.453
4dbs0HVAldo-keto reductase family 1 member C3/0.453
4iaq2GM5-hydroxytryptamine receptor 1B/0.452
4jbtASDCytochrome P450 monooxygenase/0.452
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.451
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.451
4j6bPLOCytochrome P450 monooxygenase/0.451
4nt3ZAWLactoperoxidase1.11.1.70.451
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
2po3T4K4-dehydrase/0.450
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.449
2geuCOKPantothenate kinase2.7.1.330.449
2qimZEAClass 10 plant pathogenesis-related protein/0.449
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.449
4u140HKMuscarinic acetylcholine receptor M3/0.449
1drfFOLDihydrofolate reductase1.5.1.30.448
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1z6tADPApoptotic protease-activating factor 1/0.448
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.448
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1pkfEPDEpothilone C/D epoxidase1.140.447
3hv3R49Mitogen-activated protein kinase 14/0.447
3k47D09Dihydrofolate reductase1.5.1.30.447
4fam0SZAldo-keto reductase family 1 member C3/0.447
2w3mFOLDihydrofolate reductase1.5.1.30.446
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.446
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.446
1h35R01Squalene--hopene cyclase4.2.1.1290.445
3cqeP91Wee1-like protein kinase2.7.10.20.445
3h4vDVPPteridine reductase 11.5.1.330.445
3tdaPN0Cytochrome P450 2D6/0.445
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.445
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.444
4bb3KKAIsopenicillin N synthase1.21.3.10.444
4jtrIZPAldo-keto reductase family 1 member C2/0.444
5a4vQUEGlutathione S-transferase F22.5.1.180.444
5bn4ANPV-type ATP synthase alpha chain/0.444
3uzcT4EAdenosine receptor A2a/0.444
1yplRA8Prothrombin3.4.21.50.443
3zkuHCVIsopenicillin N synthase1.21.3.10.443
1pq944BOxysterols receptor LXR-beta/0.442
1zdwFLVPrenyltransferase/0.442
3arvSAUChitinase A/0.442
3lfeZ84Mitogen-activated protein kinase 14/0.442
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.442
4paaTHGDimethylglycine dehydrogenase, mitochondrial1.5.8.40.442
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2io6330Wee1-like protein kinase2.7.10.20.441
3g72A6TRenin3.4.23.150.441
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
4jlk1NODeoxycytidine kinase2.7.1.740.441
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.440
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.440
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.440
3s7a684Dihydrofolate reductase1.5.1.30.440
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.440
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.440