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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
3b9gIMHIAG-nucleoside hydrolase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3b9gIMHIAG-nucleoside hydrolase/1.000
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.495
1kicNOSIAG-nucleoside hydrolase/0.491
2j7cIDEBeta-glucosidase A3.2.1.210.484
4jpg1OXPyruvate kinase PKM2.7.1.400.483
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.480
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.477
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.475
2pb1NFGGlucan 1,3-beta-glucosidase/0.475
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.474
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.474
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.473
1ry0PG2Aldo-keto reductase family 1 member C3/0.470
1xf0ASDAldo-keto reductase family 1 member C3/0.468
1kieAD3IAG-nucleoside hydrolase/0.467
2gg3U13Methionine aminopeptidase/0.467
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.467
1e1fPSG4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.466
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.465
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.465
2gg0U11Methionine aminopeptidase/0.465
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.465
3burTES3-oxo-5-beta-steroid 4-dehydrogenase/0.464
3epxIMQIAG-nucleoside hydrolase/0.463
3gyf51PDihydrofolate reductase1.5.1.30.463
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.462
1lnmDTXBilin-binding protein/0.462
2xi4AFTAcetylcholinesterase3.1.1.70.461
2xuhTZ4Acetylcholinesterase3.1.1.70.461
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.461
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.460
2xlpNAPPutative flavin-containing monooxygenase/0.460
5dp2NAPCurF/0.460
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
2vq7NAPPutative flavin-containing monooxygenase/0.459
3ug8IMNAldo-keto reductase family 1 member C3/0.459
5cxv0HKMuscarinic acetylcholine receptor M1/0.458
2cekN8TAcetylcholinesterase3.1.1.70.457
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.457
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.457
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.457
3zj6VM2Raucaffricine-O-beta-D-glucosidase3.2.1.1250.457
4b7zQ4QAcetylcholinesterase3.1.1.70.457
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.457
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.457
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.457
4wx2F6FTryptophan synthase alpha chain/0.457
4wx2F6FTryptophan synthase beta chain4.2.1.200.457
2w6cBM4Acetylcholinesterase3.1.1.70.456
1s1rNAPAldo-keto reductase family 1 member C3/0.455
4fouC2EUncharacterized protein/0.455
1zgbA1EAcetylcholinesterase3.1.1.70.454
1pfyMSPMethionine--tRNA ligase6.1.1.100.453
2ha6SCKAcetylcholinesterase3.1.1.70.453
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.453
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.453
4mbsMRVC-C chemokine receptor type 5/0.453
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.452
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.452
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
2xugTZ4Acetylcholinesterase3.1.1.70.451
1e7wMTXPteridine reductase 11.5.1.330.450
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.450
1k8zIAGTryptophan synthase alpha chain/0.449
1obnASVIsopenicillin N synthase1.21.3.10.449
2cleF6FTryptophan synthase alpha chain/0.449
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.449
2vrjNCWBeta-glucosidase A3.2.1.210.449
1d3dBZTProthrombin3.4.21.50.448
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.448
2xltNA0Putative flavin-containing monooxygenase/0.448
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
2a3bCFFEndochitinase B13.2.1.140.447
3ugrIMNAldo-keto reductase family 1 member C3/0.447
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.447
5a4wQCTGlutathione S-transferase F22.5.1.180.447
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.446
1odcA8BAcetylcholinesterase3.1.1.70.446
1pg0MODMethionine--tRNA ligase6.1.1.100.446
2iqdLPAAldose reductase1.1.1.210.446
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.446
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.446
4n1fCZHObelin/0.446
4u140HKMuscarinic acetylcholine receptor M3/0.446
1el4CTZObelin/0.445
1p0pBCHCholinesterase3.1.1.80.445
2d06ESTSulfotransferase 1A12.8.2.10.445
2j7dGI1Beta-glucosidase A3.2.1.210.445
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.445
3v94WYQPhosphodiesterase/0.445
4arbC57Acetylcholinesterase3.1.1.70.445
4fam0SZAldo-keto reductase family 1 member C3/0.445
4mqt2CUMuscarinic acetylcholine receptor M2/0.445
2g6pHM2Methionine aminopeptidase 1/0.444
2zevIPEGeranylgeranyl pyrophosphate synthase/0.444
5cc9DDFDihydrofolate reductase1.5.1.30.444
1zgcA2EAcetylcholinesterase3.1.1.70.443
2v5uFMNFlavodoxin/0.443
3f3y4OABile salt sulfotransferase2.8.2.140.443
4hrqAZGCytidine and deoxycytidylate deaminase zinc-binding region/0.443
4n65FMNFMN-dependent NADH-azoreductase 1/0.443
4u150HKMuscarinic acetylcholine receptor M3/0.443
1ah3TOLAldose reductase1.1.1.210.442
1eveE20Acetylcholinesterase3.1.1.70.442
1qv0CZHObelin/0.442
1u65CP0Acetylcholinesterase3.1.1.70.442
1vp5NAPOxidoreductase, aldo/keto reductase family/0.442
2xuqTZ4Acetylcholinesterase3.1.1.70.442
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4dz5NAPAldo-keto reductase family 1 member C3/0.442
4j7hTRHPCZA361.3/0.442
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.442
1e66HUXAcetylcholinesterase3.1.1.70.441
1w4lGL8Acetylcholinesterase3.1.1.70.441
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.441
2j3qTFLAcetylcholinesterase3.1.1.70.441
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.441
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.441
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
4br3U85Choline kinase alpha2.7.1.320.441
5c1mCLRMu-type opioid receptor/0.441
1d3pBT3Prothrombin3.4.21.50.440
1dpmEBPParathion hydrolase3.1.8.10.440
2bsxNOSPurine nucleoside phosphorylase/0.440
2hzqSTRApolipoprotein D/0.440
2jf0HBPAcetylcholinesterase3.1.1.70.440
2pdlTOLAldose reductase1.1.1.210.440
3ihgVAKAklavinone 12-hydroxylase RdmE/0.440
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.440