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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
3t2wBTNAvidin/streptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3t2wBTNAvidin/streptavidin/1.000
1srhMOBStreptavidin/0.599
1lcwSHMStreptavidin/0.581
2rtmIMIStreptavidin/0.579
2izhBTNStreptavidin/0.575
4bx7B4FStreptavidin/0.567
2rtgBTNStreptavidin/0.566
4dneDTBStreptavidin/0.564
2rtfBTNStreptavidin/0.562
3ry2BTNStreptavidin/0.553
2izgBTNStreptavidin/0.546
2rtnIMIStreptavidin/0.542
1srfMTBStreptavidin/0.537
4gdaBTNStreptavidin/0.535
1mk5BTNStreptavidin/0.532
1sreHABStreptavidin/0.531
2izfBTNStreptavidin/0.531
2rtdBTNStreptavidin/0.531
3wznBTNStreptavidin/0.529
1df8BTNStreptavidin/0.525
2izjBTNStreptavidin/0.524
2rtoIMIStreptavidin/0.524
1sriDMBStreptavidin/0.519
2izlIMIStreptavidin/0.519
1luqBTNStreptavidin/0.518
1lczBH7Streptavidin/0.517
2rtpIMIStreptavidin/0.517
2rtqIMIStreptavidin/0.517
2rteBTNStreptavidin/0.516
2rtrIMIStreptavidin/0.516
3ew2BTNHypothetical conserved protein/0.516
1swtBTNStreptavidin/0.514
2rtiGLLStreptavidin/0.514
2izkGLLStreptavidin/0.513
2fhnBNIAvidin-related protein 4/5/0.511
3wyqBTNStreptavidin/0.509
1i9hBNIStreptavidin/0.501
4psbGA3Cytokinin-specific binding protein/0.498
1srgMHBStreptavidin/0.497
1swpBTQStreptavidin/0.497
2aviBTNAvidin/0.497
1nqmBTNStreptavidin/0.494
4a81DXCMajor pollen allergen Bet v 1-A/0.494
4ggzBTNBll1558 protein/0.494
5stdUNNScytalone dehydratase4.2.1.940.493
1srjNABStreptavidin/0.492
1nc9IMIStreptavidin/0.490
4z28BTNHoefavidin/0.490
2y3fBTNStreptavidin/0.488
3h3sH15Collagen type IV alpha-3-binding protein/0.486
2c4iBTNAvidin/0.484
1rxhBNIStreptavidin/0.483
4a83DXCMajor pollen allergen Bet v 1-A/0.481
1swnBTNStreptavidin/0.478
3h3r14HCollagen type IV alpha-3-binding protein/0.476
1avdBTNAvidin/0.475
1ndjBTNStreptavidin/0.473
3bk2U5PRibonuclease J/0.472
1stpBTNStreptavidin/0.471
2iziBTNStreptavidin/0.471
1sweBTNStreptavidin/0.470
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.469
2uxoTACHTH-type transcriptional regulator TtgR/0.469
1n43BTNStreptavidin/0.468
1swpBTNStreptavidin/0.468
3g7jGTXGlutathione transferase GST1-4/0.467
4u140HKMuscarinic acetylcholine receptor M3/0.467
3h3qH13Collagen type IV alpha-3-binding protein/0.466
1hb1OCVIsopenicillin N synthase1.21.3.10.465
2npfMOUElongation factor 2/0.465
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.465
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
1hb3SCVIsopenicillin N synthase1.21.3.10.463
2uywBTNAvd protein/0.462
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.462
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
1n9mBTNStreptavidin/0.461
2rtlIMIStreptavidin/0.461
3h3t16HCollagen type IV alpha-3-binding protein/0.461
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.460
4bb3KKAIsopenicillin N synthase1.21.3.10.459
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.458
3rdqDTBStreptavidin/0.458
2jb4A14Isopenicillin N synthase1.21.3.10.457
1x2eATXProline iminopeptidase3.4.11.50.456
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2cdaNAPGlucose 1-dehydrogenase/0.455
2oegUPGUDP-glucose pyrophosphorylase/0.454
2po7CHDFerrochelatase, mitochondrial4.99.1.10.454
2zscBTNTamavidin2/0.454
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.454
4bj8BTNAvidin/0.454
1je1GMPPurine nucleoside phosphorylase/0.453
2yhuWHFPteridine reductase/0.453
1n0uSO1Elongation factor 2/0.452
3nmpPYVAbscisic acid receptor PYL2/0.452
1obnASVIsopenicillin N synthase1.21.3.10.451
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.451
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2iviACWIsopenicillin N synthase1.21.3.10.450
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
4a86H35Major pollen allergen Bet v 1-A/0.450
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
3dcwEZLCarbonic anhydrase 24.2.1.10.449
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
4uugPXGBranched-chain amino acid aminotransferase, putative/0.448
4bcsBTNAvidin-related protein 4/5/0.446
8catNDPCatalase1.11.1.60.446
1rx7FOLDihydrofolate reductase1.5.1.30.445
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.445
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.445
3fhxPLPPyridoxal kinase2.7.1.350.444
3k4nFADPyranose 2-oxidase/0.444
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4kak06UDihydrofolate reductase1.5.1.30.444
2mjpANPdITP/XTP pyrophosphatase3.6.1.190.443
2zs8ADPPantothenate kinase2.7.1.330.443
4u7wNDPMxaA/0.443
1mrqSTRAldo-keto reductase family 1 member C1/0.442
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.442
3ho2N323-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.442
4h6pFMNChromate reductase/0.442
4ixeIXEDihydrofolate reductase1.5.1.30.442
1gky5GPGuanylate kinase2.7.4.80.441
1lkeDOGBilin-binding protein/0.441
1pqc444Oxysterols receptor LXR-beta/0.441
2r0cFADPutative FAD-monooxygenase/0.441
2y60M8FIsopenicillin N synthase1.21.3.10.441
3owuEQUSteroid Delta-isomerase5.3.3.10.441
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.441
1swrBTNStreptavidin/0.440
2xlrNAPPutative flavin-containing monooxygenase/0.440
3ptzUDXUDP-glucose 6-dehydrogenase1.1.1.220.440
4bfzZVZPantothenate kinase2.7.1.330.440