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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
3qi1C6ABeta-secretase 13.4.23.46

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3qi1C6ABeta-secretase 13.4.23.461.000
4i0j842Beta-secretase 13.4.23.460.610
4ke11R6Beta-secretase 13.4.23.460.608
4i0h1BLBeta-secretase 13.4.23.460.591
3cib314Beta-secretase 13.4.23.460.590
4dpf0LGBeta-secretase 13.4.23.460.579
3n4l842Beta-secretase 13.4.23.460.577
1xs7MMIBeta-secretase 13.4.23.460.575
2g94ZPQBeta-secretase 13.4.23.460.570
2f3eAXQBeta-secretase 13.4.23.460.569
3k5fAYHBeta-secretase 13.4.23.460.569
4djy0KRBeta-secretase 13.4.23.460.569
2hizLIJBeta-secretase 13.4.23.460.566
2fdpFRPBeta-secretase 13.4.23.460.562
2hm1LIQBeta-secretase 13.4.23.460.558
4ke01R8Beta-secretase 13.4.23.460.556
3duyAFJBeta-secretase 13.4.23.460.554
3k5dXLIBeta-secretase 13.4.23.460.554
3k5gBJCBeta-secretase 13.4.23.460.553
4lxa1YSBeta-secretase 13.4.23.460.553
4dh60KNBeta-secretase 13.4.23.460.552
4lxk1YTBeta-secretase 13.4.23.460.552
4k8s1QTBeta-secretase 13.4.23.460.549
2p83MR0Beta-secretase 13.4.23.460.548
3nsh957Beta-secretase 13.4.23.460.547
4i0i957Beta-secretase 13.4.23.460.547
2f3fAXFBeta-secretase 13.4.23.460.546
3lpjZ75Beta-secretase 13.4.23.460.545
3r2fPB0Beta-secretase 13.4.23.460.545
4exg916Beta-secretase 13.4.23.460.545
3lpkZ76Beta-secretase 13.4.23.460.542
4d89BXDBeta-secretase 13.4.23.460.542
3dv1AR9Beta-secretase 13.4.23.460.541
3ixj586Beta-secretase 13.4.23.460.541
2vkmBSDBeta-secretase 13.4.23.460.538
3exo5MSBeta-secretase 13.4.23.460.538
3cid318Beta-secretase 13.4.23.460.536
3fktSIIBeta-secretase 13.4.23.460.534
3cic316Beta-secretase 13.4.23.460.533
3ohf3HFBeta-secretase 13.4.23.460.532
4fse0VABeta-secretase 13.4.23.460.532
4h3f10OBeta-secretase 13.4.23.460.532
4lxm1YUBeta-secretase 13.4.23.460.532
4ewo996Beta-secretase 13.4.23.460.531
2iqgF2IBeta-secretase 13.4.23.460.530
4i1c1BEBeta-secretase 13.4.23.460.527
3ixk929Beta-secretase 13.4.23.460.526
3qbhQBHBeta-secretase 13.4.23.460.525
1tqf32PBeta-secretase 13.4.23.460.524
2ph835ABeta-secretase 13.4.23.460.524
3skgPB8Beta-secretase 13.4.23.460.523
1w51L01Beta-secretase 13.4.23.460.520
1w6hTITPlasmepsin-23.4.23.390.520
4h3j10WBeta-secretase 13.4.23.460.520
3veu0GOBeta-secretase 13.4.23.460.518
2ntrL00Beta-secretase 13.4.23.460.517
3d91REMRenin3.4.23.150.516
2irzI02Beta-secretase 13.4.23.460.515
2vijC44Beta-secretase 13.4.23.460.515
3lpiZ74Beta-secretase 13.4.23.460.515
3t7x4SHEndothiapepsin3.4.23.220.515
4dus0MPBeta-secretase 13.4.23.460.515
4gid0GHBeta-secretase 13.4.23.460.515
2p4j23IBeta-secretase 13.4.23.460.514
4fco0U4Beta-secretase 13.4.23.460.512
2wf1ZY1Beta-secretase 13.4.23.460.511
4l7g1W0Beta-secretase 13.4.23.460.511
2ph6712Beta-secretase 13.4.23.460.510
4fs4H24Beta-secretase 13.4.23.460.509
2qzlIXSBeta-secretase 13.4.23.460.508
3dm6757Beta-secretase 13.4.23.460.508
2oahQINBeta-secretase 13.4.23.460.507
4k9h1QUBeta-secretase 13.4.23.460.507
4b722FBBeta-secretase 13.4.23.460.505
4b78KGGBeta-secretase 13.4.23.460.503
2vieVG0Beta-secretase 13.4.23.460.502
3vf30GSBeta-secretase 13.4.23.460.502
2g247IGRenin3.4.23.150.501
2il2LIXRenin3.4.23.150.501
2g1n1IGRenin3.4.23.150.499
2g21L1BRenin3.4.23.150.499
3own3OXRenin3.4.23.150.499
2vnmCM8Beta-secretase 13.4.23.460.498
2wf3ZY3Beta-secretase 13.4.23.460.498
3t6iNC9Endothiapepsin3.4.23.220.498
1bim0QBRenin3.4.23.150.497
4b70WM9Beta-secretase 13.4.23.460.497
2i4qUA4Renin3.4.23.150.496
4dpi0N1Beta-secretase 13.4.23.460.496
2b8l5HABeta-secretase 13.4.23.460.495
2ikuLIYRenin3.4.23.150.494
2p8hMY9Beta-secretase 13.4.23.460.494
4j1f1HLBeta-secretase 13.4.23.460.494
2is0I03Beta-secretase 13.4.23.460.493
2xfiXFIBeta-secretase 13.4.23.460.493
4fm80UQBeta-secretase 13.4.23.460.493
2g1r3IGRenin3.4.23.150.490
2xfjVG5Beta-secretase 13.4.23.460.490
4b0qGMFBeta-secretase 13.4.23.460.490
2g1o2IGRenin3.4.23.150.489
1rneC60Renin3.4.23.150.487
2g20L1ARenin3.4.23.150.487
3tpr5HABeta-secretase 13.4.23.460.487
4lc71WPBeta-secretase 13.4.23.460.486
2vj7VG6Beta-secretase 13.4.23.460.485
2vnnCM7Beta-secretase 13.4.23.460.485
4b1c1B1Beta-secretase 13.4.23.460.485
4j1k1HGBeta-secretase 13.4.23.460.485
2wf2ZY2Beta-secretase 13.4.23.460.484
2b8v3BNBeta-secretase 13.4.23.460.483
2wf0ZY0Beta-secretase 13.4.23.460.483
2wf4ZY4Beta-secretase 13.4.23.460.481
1xe55FEPlasmepsin-23.4.23.390.480
2g1s4IGRenin3.4.23.150.479
3vucHHERenin3.4.23.150.479
1psa0ZLPepsin A3.4.23.10.478
3lqfNADGalactitol dehydrogenase/0.477
3own3OWRenin3.4.23.150.477
4ha513WBeta-secretase 13.4.23.460.477
2wezZYEBeta-secretase 13.4.23.460.476
3zlq6T9Beta-secretase 23.4.23.450.476
1gvv0GMEndothiapepsin3.4.23.220.475
1xe65FPPlasmepsin-23.4.23.390.475
3vswR31Renin3.4.23.150.475
2g263LGRenin3.4.23.150.474
3kmxG00Beta-secretase 13.4.23.460.474
1lf3EH5Plasmepsin-23.4.23.390.473
4djx0KQBeta-secretase 13.4.23.460.473
4frkDWDBeta-secretase 13.4.23.460.473
2v16C47Renin3.4.23.150.472
3i25MV7Beta-secretase 13.4.23.460.472
3pwwROCEndothiapepsin3.4.23.220.472
1bil0IURenin3.4.23.150.471
1gvt2ZSEndothiapepsin3.4.23.220.470
3vydVYDRenin3.4.23.150.470
3gqvNAPEnoyl reductase LovC10.469
4yaoFMNNADPH--cytochrome P450 reductase/0.469
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.468
2lfoGCHFatty acid-binding protein, liver/0.468
4b7754MBeta-secretase 13.4.23.460.468
4yfy1YJVioF/0.467
3gwfNAPCyclohexanone monooxygenase/0.466
4frs0V6Beta-secretase 13.4.23.460.466
2v13C40Renin3.4.23.150.465
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
2g226IGRenin3.4.23.150.464
3tneRITCandidapepsin-13.4.23.240.463
3udn09BBeta-secretase 13.4.23.460.463
4l7j1W2Beta-secretase 13.4.23.460.463
2iko7IGRenin3.4.23.150.462
3oqkS52Renin3.4.23.150.462
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.462
2v00V15Endothiapepsin3.4.23.220.461
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.461
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.460
4bfzZVZPantothenate kinase2.7.1.330.460
1gvw0EMEndothiapepsin3.4.23.220.459
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3oqfS51Renin3.4.23.150.458
4azy7F3Beta-secretase 13.4.23.460.457
4y3zF41Endothiapepsin3.4.23.220.457
2q153MRBeta-secretase 13.4.23.460.456
2vj6VG5Beta-secretase 13.4.23.460.456
4y380A9Endothiapepsin3.4.23.220.456
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3vyfVYFRenin3.4.23.150.455
4h3i10VBeta-secretase 13.4.23.460.455
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.455
1e800GQEndothiapepsin3.4.23.220.454
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.454
2xfkAA9Beta-secretase 13.4.23.460.454
1cjuFOKAdenylate cyclase type 2/0.453
1cjuFOKAdenylate cyclase type 5/0.453
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
2fs4PZ1Renin3.4.23.150.452
2iyfERYOleandomycin glycosyltransferase2.4.10.452
2vizVG4Beta-secretase 13.4.23.460.452
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3h3t16HCollagen type IV alpha-3-binding protein/0.451
4j0y1H6Beta-secretase 13.4.23.460.451
4zeaIMIEndothiapepsin3.4.23.220.451
2bjfDXCCholoylglycine hydrolase3.5.1.240.450
3pbzF02Endothiapepsin3.4.23.220.450
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1od10QSEndothiapepsin3.4.23.220.449
2g1y5IGRenin3.4.23.150.449
1hdoNAPFlavin reductase (NADPH)/0.448
1ppkIVVPenicillopepsin-13.4.23.200.448
1t2cNAIL-lactate dehydrogenase1.1.1.270.448
3vsxR32Renin3.4.23.150.448
4dptAGSMevalonate diphosphate decarboxylase/0.448
4y3qF02Endothiapepsin3.4.23.220.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3adaNADSubunit alpha of sarocosine oxidase/0.447
3oagLPQRenin3.4.23.150.447
3g6zA7TRenin3.4.23.150.446
3oadLPORenin3.4.23.150.446
3psyRB9Endothiapepsin3.4.23.220.446
3t7qRB4Endothiapepsin3.4.23.220.446
3zkiWZVBeta-secretase 23.4.23.450.446
4h6pFMNChromate reductase/0.446
1zapA70Candidapepsin-23.4.23.240.445
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.445
2g274LGRenin3.4.23.150.445
2wedPP6Penicillopepsin-13.4.23.200.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
3pw8ACO1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.445
3t6iNC8Endothiapepsin3.4.23.220.445
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
4dju0KKBeta-secretase 13.4.23.460.445
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.445
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.445
2bn4FMNNADPH--cytochrome P450 reductase/0.444
2vj9VG7Beta-secretase 13.4.23.460.444
3g70A5TRenin3.4.23.150.444
3lqsPSZD-alanine aminotransferase2.6.1.210.444
3zeiAWHO-acetylserine sulfhydrylase/0.444
4acuQN7Beta-secretase 13.4.23.460.444
4j0v1H7Beta-secretase 13.4.23.460.444
4uymVOR14-alpha sterol demethylase Cyp51B/0.444
2gjlFMNNitronate monooxygenase1.13.12.160.443
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4bfxZVXPantothenate kinase2.7.1.330.443
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.443
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.443
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4bfvZVVPantothenate kinase2.7.1.330.442
4fsl0VBBeta-secretase 13.4.23.460.442
1bxoPP7Penicillopepsin-13.4.23.200.441
1bxqPP8Penicillopepsin-13.4.23.200.441
3drcMTXDihydrofolate reductase1.5.1.30.441
3prsRITEndothiapepsin3.4.23.220.441
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.441
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.441
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.441
4r21STRCytochrome P450 family 17 polypeptide 2/0.441
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.441
4y1bNAPAntE/0.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.440
3pi0F91Endothiapepsin3.4.23.220.440
3rupADPBiotin carboxylase6.3.4.140.440
4bekXK0Beta-secretase 13.4.23.460.440
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.440
4m83ERYOleandomycin glycosyltransferase2.4.10.440
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.440