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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
1n9mBTNStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1n9mBTNStreptavidin/1.000
1swnBTNStreptavidin/0.634
1sweBTNStreptavidin/0.592
1nc9IMIStreptavidin/0.581
1mepBTNStreptavidin/0.580
1swpBTQStreptavidin/0.562
1swdBTNStreptavidin/0.561
4gd9BTNStreptavidin/0.561
1ndjBTNStreptavidin/0.558
1n43BTNStreptavidin/0.556
1swpBTNStreptavidin/0.554
4yvbBTNStreptavidin/0.546
1stpBTNStreptavidin/0.542
2zscBTNTamavidin2/0.539
2rtgBTNStreptavidin/0.537
2y3fBTNStreptavidin/0.536
3wypBSOStreptavidin/0.536
1lcwSHMStreptavidin/0.531
3ry2BTNStreptavidin/0.531
4bx7B4FStreptavidin/0.527
1srfMTBStreptavidin/0.524
2izfBTNStreptavidin/0.524
4ggzBTNBll1558 protein/0.521
2izhBTNStreptavidin/0.519
1sreHABStreptavidin/0.513
2fhnBNIAvidin-related protein 4/5/0.513
2rtoIMIStreptavidin/0.513
1sriDMBStreptavidin/0.511
4dneDTBStreptavidin/0.511
2rtqIMIStreptavidin/0.508
2rtfBTNStreptavidin/0.505
1obnASVIsopenicillin N synthase1.21.3.10.501
1rxhBNIStreptavidin/0.501
2rtpIMIStreptavidin/0.501
4bj8BTNAvidin/0.500
2rtnIMIStreptavidin/0.498
1srgMHBStreptavidin/0.497
2rtrIMIStreptavidin/0.497
1mk5BTNStreptavidin/0.494
2izgBTNStreptavidin/0.494
2rtdBTNStreptavidin/0.494
3zkyWT4Isopenicillin N synthase1.21.3.10.489
2vbpVB1Isopenicillin N synthase1.21.3.10.484
1oc1ASVIsopenicillin N synthase1.21.3.10.483
2izlIMIStreptavidin/0.483
1hb3SCVIsopenicillin N synthase1.21.3.10.480
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.480
1srjNABStreptavidin/0.480
3vhiVHIAvidin/0.480
1swtBTNStreptavidin/0.479
3vhmNPKAvidin/0.479
1df8BTNStreptavidin/0.477
2vcmM11Isopenicillin N synthase1.21.3.10.475
3wyqBTNStreptavidin/0.475
2wo7ASVIsopenicillin N synthase1.21.3.10.474
1srhMOBStreptavidin/0.473
1swrBTNStreptavidin/0.473
2rteBTNStreptavidin/0.472
4gdaBTNStreptavidin/0.472
2y6fM9FIsopenicillin N synthase1.21.3.10.470
4bb3KKAIsopenicillin N synthase1.21.3.10.470
1blzACVIsopenicillin N synthase1.21.3.10.469
1qjfACSIsopenicillin N synthase1.21.3.10.468
2rtmIMIStreptavidin/0.467
3zoiM2WIsopenicillin N synthase1.21.3.10.467
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.466
2y60M8FIsopenicillin N synthase1.21.3.10.465
1fvpFMANon-fluorescent flavoprotein/0.462
2jgsBTNAvidin/0.462
1g63FMNEpidermin decarboxylase4.1.10.461
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.461
2aviBTNAvidin/0.461
3rdqDTBStreptavidin/0.461
1nqmBTNStreptavidin/0.460
2iziBTNStreptavidin/0.457
2vkeTACTetracycline repressor protein class D/0.457
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.456
3wznBTNStreptavidin/0.455
1luqBTNStreptavidin/0.454
1w06W05Isopenicillin N synthase1.21.3.10.454
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.454
2iviACWIsopenicillin N synthase1.21.3.10.454
1jjeBYSBeta-lactamase/0.453
1qiqACCIsopenicillin N synthase1.21.3.10.453
3h4vDVPPteridine reductase 11.5.1.330.453
4bcsBTNAvidin-related protein 4/5/0.453
1pq944BOxysterols receptor LXR-beta/0.452
2c4iBTNAvidin/0.452
4e2zJHZMethyltransferase/0.452
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.452
1odnAPVIsopenicillin N synthase1.21.3.10.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
3vgwNVZAvidin/0.451
4jq3NAPAldo-keto reductase family 1 member C2/0.451
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.450
4phlPILPhosphodiesterase/0.450
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.449
4bj9UHBTankyrase-22.4.2.300.449
1ygkRRCPyridoxal kinase2.7.1.350.448
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.448
4fam0SZAldo-keto reductase family 1 member C3/0.448
1ta6177Prothrombin3.4.21.50.447
2w6mOA1Biotin carboxylase6.3.4.140.447
2x7hPFNProstaglandin reductase 310.447
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.447
4kwhNAPReductase homolog/0.447
4xczT3QQdtf/0.447
1hb1OCVIsopenicillin N synthase1.21.3.10.446
2uz2BTNAvd protein/0.446
3ndjJHZMethyltransferase/0.446
3wqmB29Diterpene synthase3.1.7.80.446
4li81XQTankyrase-12.4.2.300.446
2vbdV10Isopenicillin N synthase1.21.3.10.445
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.445
3vhhVHHAvidin/0.445
4l091URTankyrase-22.4.2.300.445
4lsaBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.445
4n4v2GYTankyrase-12.4.2.300.445
1d3pBT3Prothrombin3.4.21.50.444
1ezfIN0Squalene synthase2.5.1.210.444
2g263LGRenin3.4.23.150.444
4jtqNAPAldo-keto reductase family 1 member C2/0.444
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.444
5a4vQUEGlutathione S-transferase F22.5.1.180.444
1avdBTNAvidin/0.443
1s3uTQDDihydrofolate reductase1.5.1.30.443
2dvlFADAcyl-CoA dehydrogenase/0.443
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.443
1bk0ACVIsopenicillin N synthase1.21.3.10.442
1c7oPPGHemolysin/0.442
1d6w00RProthrombin3.4.21.50.442
1ogiFADFerredoxin--NADP reductase1.18.1.20.442
1re0AFBADP-ribosylation factor 1/0.442
1re0AFBARF guanine-nucleotide exchange factor 1/0.442
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.442
2hdjNDPAldo-keto reductase family 1 member C2/0.442
4bftZVTPantothenate kinase2.7.1.330.442
4du6GTPGTP cyclohydrolase 1/0.442
1lczBH7Streptavidin/0.441
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1ygjRMCPyridoxal kinase2.7.1.350.441
1z7yAA5Cysteine synthase 12.5.1.470.441
2xlrFADPutative flavin-containing monooxygenase/0.441
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4yfy0FXVioF/0.441
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.441
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.440
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.440
4n3l2FNProthrombin3.4.21.50.440
4pnmNU1Tankyrase-22.4.2.300.440