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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
3emzHXHEndo-1,4-beta-xylanase B3.2.1.8

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3emzHXHEndo-1,4-beta-xylanase B3.2.1.81.000
3cuiX4SExoglucanase/xylanase3.2.1.910.648
2j7cIDEBeta-glucosidase A3.2.1.210.482
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.481
2gg8U15Methionine aminopeptidase/0.481
2y1w849Histone-arginine methyltransferase CARM1/0.480
3zj6VM2Raucaffricine-O-beta-D-glucosidase3.2.1.1250.480
4s1iPLPPyridoxal kinase, putative/0.479
4br3U85Choline kinase alpha2.7.1.320.478
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.475
2y0468HBeta-1 adrenergic receptor/0.475
2z7gEH9Adenosine deaminase3.5.4.40.468
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.467
2xuhTZ4Acetylcholinesterase3.1.1.70.466
1e1fPSG4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.465
2ggbU17Methionine aminopeptidase/0.464
2f2hXTGAlpha-xylosidase3.2.1.1770.463
3zwxAV1ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase3.2.2.60.463
3burTES3-oxo-5-beta-steroid 4-dehydrogenase/0.462
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.461
3i9jNFDADP-ribosyl cyclase/cyclic ADP-ribose hydrolase3.2.2.60.461
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.460
3i9kNADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase3.2.2.60.460
3n0hTOPDihydrofolate reductase1.5.1.30.460
4ey7E20Acetylcholinesterase3.1.1.70.460
4nv14TGFormyl transferase/0.460
2a3bCFFEndochitinase B13.2.1.140.459
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.459
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.459
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.458
3vilSA0Beta-glucosidase/0.457
1ry0PG2Aldo-keto reductase family 1 member C3/0.456
3ptqNFGBeta-glucosidase 12/0.456
1wkgPOI[LysW]-aminoadipate semialdehyde transaminase/0.455
2pdu393Aldose reductase1.1.1.210.455
3iu9T07Methionine aminopeptidase 2/0.455
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.455
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.455
5jqhCAUBeta-2 adrenergic receptor/0.455
1u8xNADMaltose-6'-phosphate glucosidase3.2.1.1220.454
1w6rGNTAcetylcholinesterase3.1.1.70.454
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.454
2hzqSTRApolipoprotein D/0.453
3ug8IMNAldo-keto reductase family 1 member C3/0.453
4b1e6T6Beta-secretase 13.4.23.460.453
2aotSAHHistamine N-methyltransferase2.1.1.80.452
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.452
2j7dGI1Beta-glucosidase A3.2.1.210.452
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.452
3udj092Beta-secretase 13.4.23.460.452
3uonQNBMuscarinic acetylcholine receptor M2/0.452
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2iki388Aldose reductase1.1.1.210.450
2xysSY9Soluble acetylcholine receptor/0.449
4u163C0Muscarinic acetylcholine receptor M3/0.449
2oymMNIEndoglycoceramidase II/0.448
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.448
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4cg8G8SCholine kinase alpha2.7.1.320.448
4fam0SZAldo-keto reductase family 1 member C3/0.448
3ny8JRZBeta-2 adrenergic receptor/0.448
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.447
4a7zAY9Aldos-2-ulose dehydratase/0.447
4b7zQ4QAcetylcholinesterase3.1.1.70.447
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.446
2gg3U13Methionine aminopeptidase/0.446
2gywOBIAcetylcholinesterase3.1.1.70.446
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.446
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.446
3f90FMNFlavodoxin/0.446
3rsv3RSBeta-secretase 13.4.23.460.446
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.445
1pr6XYAPurine nucleoside phosphorylase DeoD-type/0.445
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.445
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.445
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.445
1obnASVIsopenicillin N synthase1.21.3.10.444
2fz8ZSTAldose reductase1.1.1.210.444
2ha6SCKAcetylcholinesterase3.1.1.70.444
2p99YE6Methionine aminopeptidase/0.444
2vqqTFGHistone deacetylase 43.5.1.980.444
2weaPP6Penicillopepsin-13.4.23.200.444
4kn104JFolate receptor beta/0.444
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.444
2pb1NFGGlucan 1,3-beta-glucosidase/0.443
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.443
3v35NTIAldose reductase1.1.1.210.443
3zecANPAdenosine monophosphate-protein transferase SoFic2.7.7.n10.443
4yfy0FXVioF/0.443
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.442
2jf0HBPAcetylcholinesterase3.1.1.70.442
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.442
4amjCVDBeta-1 adrenergic receptor/0.442
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.442
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
1pke2FDPurine nucleoside phosphorylase DeoD-type/0.441
1vp5NAPOxidoreductase, aldo/keto reductase family/0.441
2q94A04Methionine aminopeptidase/0.441
2y035FWBeta-1 adrenergic receptor/0.441
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.441
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.441
4j171HQBeta-secretase 13.4.23.460.441
4kn0MTXFolate receptor beta/0.441
5a4wQCTGlutathione S-transferase F22.5.1.180.441
1dlrMXADihydrofolate reductase1.5.1.30.440
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.440
2aot2PMHistamine N-methyltransferase2.1.1.80.440
2cekN8TAcetylcholinesterase3.1.1.70.440
3ai0PNWBeta-glucosidase/0.440
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3kmyD8YBeta-secretase 13.4.23.460.440
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.440
4lrhFOLFolate receptor alpha/0.440