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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
3iu7FCDMethionine aminopeptidase 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3iu7FCDMethionine aminopeptidase 2/1.000
3pkeY10Methionine aminopeptidase 2/0.697
2evcFC3Methionine aminopeptidase/0.624
2q94A04Methionine aminopeptidase/0.617
2evmFC2Methionine aminopeptidase/0.609
2q93B21Methionine aminopeptidase/0.609
2q92B23Methionine aminopeptidase/0.589
2p99YE6Methionine aminopeptidase/0.588
2q96A18Methionine aminopeptidase/0.587
3iu8T03Methionine aminopeptidase 2/0.585
2p98YE7Methionine aminopeptidase/0.581
3pkdY10Methionine aminopeptidase 2/0.574
3pkaY02Methionine aminopeptidase 2/0.569
2gg9U16Methionine aminopeptidase/0.568
2gg8U15Methionine aminopeptidase/0.565
2ggbU17Methionine aminopeptidase/0.564
2gg0U11Methionine aminopeptidase/0.555
3pkbY16Methionine aminopeptidase 2/0.555
1xnzFCDMethionine aminopeptidase/0.554
4flkY10Methionine aminopeptidase 1/0.551
3d27W29Methionine aminopeptidase/0.545
2g6pHM2Methionine aminopeptidase 1/0.543
1r5gAO1Methionine aminopeptidase 2/0.540
4fllYZ6Methionine aminopeptidase 1/0.540
4hxx1AYMethionine aminopeptidase 1/0.540
2gg2U12Methionine aminopeptidase/0.533
4iksTFDMethionine aminopeptidase 1/0.532
4fliY16Methionine aminopeptidase 1/0.530
4iktTFVMethionine aminopeptidase 1/0.530
2gg3U13Methionine aminopeptidase/0.529
4fljY08Methionine aminopeptidase 1/0.529
4ikuSHXMethionine aminopeptidase 1/0.529
2nq7HM5Methionine aminopeptidase 1/0.520
3pkcY08Methionine aminopeptidase 2/0.513
1yw8A75Methionine aminopeptidase 2/0.512
1c23MPHMethionine aminopeptidase/0.510
4ikrPVPMethionine aminopeptidase 1/0.506
1r58AO5Methionine aminopeptidase 2/0.493
1yw7A41Methionine aminopeptidase 2/0.485
1qzyTDEMethionine aminopeptidase 2/0.481
2ea4F79Methionine aminopeptidase 2/0.481
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.479
1amoFMNNADPH--cytochrome P450 reductase/0.477
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.477
2ea2F77Methionine aminopeptidase 2/0.475
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.475
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.474
2ga2A19Methionine aminopeptidase 2/0.468
3iu9T07Methionine aminopeptidase 2/0.468
1r5hAO2Methionine aminopeptidase 2/0.467
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.466
2oazI96Methionine aminopeptidase 2/0.461
2wzySQXSoluble acetylcholine receptor/0.461
4m0f1YKAcetylcholinesterase3.1.1.70.459
2vd7PD2Lysine-specific demethylase 4A1.14.110.458
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.458
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.457
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.456
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.456
5iefNBVNeutral alpha-glucosidase AB3.2.1.840.456
1yw9A84Methionine aminopeptidase 2/0.455
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.455
1odcA8BAcetylcholinesterase3.1.1.70.454
2qimZEAClass 10 plant pathogenesis-related protein/0.454
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.454
1mxfMTXPutative pteridine reductase 2/0.453
3af0GDPPantothenate kinase2.7.1.330.453
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.452
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.452
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.452
1h22E10Acetylcholinesterase3.1.1.70.451
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.451
2jl1NAPTriphenylmethane reductase/0.451
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.451
2xugTZ4Acetylcholinesterase3.1.1.70.450
3rsv3RSBeta-secretase 13.4.23.460.450
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.450
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.449
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.449
2gesCOKPantothenate kinase2.7.1.330.449
4gd40WSLysine-specific demethylase 4A1.14.110.449
1eveE20Acetylcholinesterase3.1.1.70.448
2aouCQAHistamine N-methyltransferase2.1.1.80.447
2xuiTZ5Acetylcholinesterase3.1.1.70.447
2xuoTZ4Acetylcholinesterase3.1.1.70.447
3g4lROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.446
3rbaCODPhosphopantetheine adenylyltransferase/0.446
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.445
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3v0p4GWHisto-blood group ABO system transferase/0.445
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.444
2j3qTFLAcetylcholinesterase3.1.1.70.444
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.444
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.444
2gv8NDPThiol-specific monooxygenase1.14.130.443
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.442
1zgbA1EAcetylcholinesterase3.1.1.70.442
2v57PRLTetR family transcriptional regulator/0.442
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
2getCOKPantothenate kinase2.7.1.330.441
2xufTZ4Acetylcholinesterase3.1.1.70.441
4zwpM44Xaa-Pro dipeptidase3.4.13.90.441
1ex75GPGuanylate kinase2.7.4.80.440
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.440
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440