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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
2d52COA5,7-dihydroxy-2-methylchromone synthase2.3.1.216

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2d52COA5,7-dihydroxy-2-methylchromone synthase2.3.1.2161.000
2d3mCOA5,7-dihydroxy-2-methylchromone synthase2.3.1.2160.794
1ee0CAA2-pyrone synthase/0.614
3wxyCOAUncharacterized protein/0.531
4jaqCOAAlpha-pyrone synthesis polyketide synthase-like Pks112.3.10.500
3wd7COAAcridone synthase/0.497
3wy0COAUncharacterized protein/0.485
1ffuFADCarbon monoxide dehydrogenase medium chain/0.473
4ly91YYGlucokinase regulatory protein/0.472
4jd3COAAlpha-pyrone synthesis polyketide synthase-like Pks112.3.10.468
1fnnADPORC1-type DNA replication protein/0.467
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.466
1bq6COAChalcone synthase 22.3.1.740.462
3kpkFADSulfide-quinone reductase/0.462
3t14FADSulfide-quinone reductase/0.462
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.458
3q8xUD1Toxin zeta/0.458
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.456
5itzLOCTubulin beta-2B chain/0.456
1kzjCB3Thymidylate synthase/0.455
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
2om9AJAPeroxisome proliferator-activated receptor gamma/0.453
3icsADPCoenzyme A disulfide reductase/0.453
4j4bNAIUncharacterized protein/0.453
2fsvNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.452
2vn0TDZCytochrome P450 2C8/0.452
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3n7uNADFormate dehydrogenase, chloroplastic/mitochondrial/0.452
4nc3ERM5-hydroxytryptamine receptor 2B/0.452
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.452
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.451
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.450
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.450
2jn3JN3Fatty acid-binding protein, liver/0.449
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.449
4enhFVXCholesterol 24-hydroxylase/0.449
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.448
4idv13VMitogen-activated protein kinase kinase kinase 142.7.11.250.448
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.448
4l3j5FIRibosomal protein S6 kinase beta-12.7.11.10.448
2vojNADAlanine dehydrogenase1.4.1.10.447
3lsiFADPyranose 2-oxidase/0.447
4ez50RSCyclin-dependent kinase 62.7.11.220.447
4ia2BIVVitamin D3 receptor A/0.447
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2nnhREACytochrome P450 2C8/0.446
2p4yC03Peroxisome proliferator-activated receptor gamma/0.446
3pvrBYC1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.446
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.446
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.446
3t2zFADSulfide-quinone reductase/0.446
3vt9YI4Vitamin D3 receptor/0.446
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
4jnm1LJNicotinamide phosphoribosyltransferase2.4.2.120.446
4lxhC1EAlpha/beta hydrolase fold/0.446
1j39UPGDNA beta-glucosyltransferase/0.445
1sn5T3Transthyretin/0.445
2oiqSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.445
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.445
3vt5YI2Vitamin D3 receptor/0.445
4ia7BIVVitamin D3 receptor A/0.445
1uumAFIDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.444
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.444
4b7dQLECytochrome P450 monooxygenase PikC/0.444
4h3c0YZDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
2rghFADAlpha-Glycerophosphate Oxidase/0.443
2y03Y01Beta-1 adrenergic receptor/0.443
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.443
4jlj1NMDeoxycytidine kinase2.7.1.740.443
1qvrANPChaperone protein ClpB/0.442
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.442
4cy8FDA2-hydroxybiphenyl-3-monooxygenase/0.442
4fidGDPG protein alpha subunit, putative/0.442
4n6bCOAUncharacterized protein/0.442
4r21STRCytochrome P450 family 17 polypeptide 2/0.442
1ie4T44Transthyretin/0.441
2y02Y01Beta-1 adrenergic receptor/0.441
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.441
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
3r374CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.441
3vt7VDXVitamin D3 receptor/0.441
4ib4ERM5-hydroxytryptamine receptor 2B/0.441
4riyADPEpidermal growth factor receptor2.7.10.10.441
5bsgNAPPyrroline-5-carboxylate reductase/0.441
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
2hk51BMTyrosine-protein kinase HCK2.7.10.20.440
2wleCOAPolysialic acid O-acetyltransferase/0.440
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.440
4kfp1R7Nicotinamide phosphoribosyltransferase2.4.2.120.440
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440