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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
3iu8T03Methionine aminopeptidase 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3iu8T03Methionine aminopeptidase 2/1.000
2evmFC2Methionine aminopeptidase/0.655
2evcFC3Methionine aminopeptidase/0.653
3iu7FCDMethionine aminopeptidase 2/0.651
2q93B21Methionine aminopeptidase/0.640
2q94A04Methionine aminopeptidase/0.640
3pkdY10Methionine aminopeptidase 2/0.633
2gg8U15Methionine aminopeptidase/0.632
3pkaY02Methionine aminopeptidase 2/0.628
3pkeY10Methionine aminopeptidase 2/0.627
2gg9U16Methionine aminopeptidase/0.626
2q92B23Methionine aminopeptidase/0.618
2q96A18Methionine aminopeptidase/0.618
4iksTFDMethionine aminopeptidase 1/0.617
3d27W29Methionine aminopeptidase/0.613
2p98YE7Methionine aminopeptidase/0.607
2gg0U11Methionine aminopeptidase/0.605
3pkbY16Methionine aminopeptidase 2/0.605
2ggbU17Methionine aminopeptidase/0.603
2gg2U12Methionine aminopeptidase/0.597
2g6pHM2Methionine aminopeptidase 1/0.592
2gg3U13Methionine aminopeptidase/0.582
1xnzFCDMethionine aminopeptidase/0.580
1c23MPHMethionine aminopeptidase/0.579
4iktTFVMethionine aminopeptidase 1/0.576
4ikuSHXMethionine aminopeptidase 1/0.575
4fliY16Methionine aminopeptidase 1/0.574
2p99YE6Methionine aminopeptidase/0.568
4hxx1AYMethionine aminopeptidase 1/0.568
2nq7HM5Methionine aminopeptidase 1/0.560
4ikrPVPMethionine aminopeptidase 1/0.557
3pkcY08Methionine aminopeptidase 2/0.554
4fllYZ6Methionine aminopeptidase 1/0.548
1r5gAO1Methionine aminopeptidase 2/0.540
3iu9T07Methionine aminopeptidase 2/0.540
4flkY10Methionine aminopeptidase 1/0.534
4fljY08Methionine aminopeptidase 1/0.529
1amoFMNNADPH--cytochrome P450 reductase/0.514
4b7zQ4QAcetylcholinesterase3.1.1.70.510
2gywOBIAcetylcholinesterase3.1.1.70.504
4m0f1YKAcetylcholinesterase3.1.1.70.503
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.497
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.497
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.497
1eveE20Acetylcholinesterase3.1.1.70.493
2ga2A19Methionine aminopeptidase 2/0.489
2j3qTFLAcetylcholinesterase3.1.1.70.488
2wzySQXSoluble acetylcholine receptor/0.488
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.488
1h22E10Acetylcholinesterase3.1.1.70.486
2xuoTZ4Acetylcholinesterase3.1.1.70.486
3mj4URMUDP-galactopyranose mutase/0.485
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.484
1yw8A75Methionine aminopeptidase 2/0.483
2oazI96Methionine aminopeptidase 2/0.483
3t0iSAHPutative methyltransferase/0.483
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.483
2pb1NFGGlucan 1,3-beta-glucosidase/0.482
2w6cBM4Acetylcholinesterase3.1.1.70.481
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.480
2vd7PD2Lysine-specific demethylase 4A1.14.110.479
1yw9A84Methionine aminopeptidase 2/0.478
1zgcA2EAcetylcholinesterase3.1.1.70.478
1qzyTDEMethionine aminopeptidase 2/0.477
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.477
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.477
1ex75GPGuanylate kinase2.7.4.80.475
1ja1FMNNADPH--cytochrome P450 reductase/0.475
1odcA8BAcetylcholinesterase3.1.1.70.475
1yw7A41Methionine aminopeptidase 2/0.475
2ea2F77Methionine aminopeptidase 2/0.475
2xupTZ5Acetylcholinesterase3.1.1.70.475
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.474
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.472
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.471
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.471
1w4lGL8Acetylcholinesterase3.1.1.70.471
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.471
4gd40WSLysine-specific demethylase 4A1.14.110.471
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.471
1u65CP0Acetylcholinesterase3.1.1.70.470
2ha6SCKAcetylcholinesterase3.1.1.70.470
2xi4AFTAcetylcholinesterase3.1.1.70.470
2xukTZ5Acetylcholinesterase3.1.1.70.470
2xuqTZ4Acetylcholinesterase3.1.1.70.470
2gyuHI6Acetylcholinesterase3.1.1.70.469
4a87NARMajor pollen allergen Bet v 1-A/0.469
4ey6GNTAcetylcholinesterase3.1.1.70.469
2xugTZ4Acetylcholinesterase3.1.1.70.468
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.468
3ziuLSSLeucyl-tRNA synthetase/0.468
1q84TZ4Acetylcholinesterase3.1.1.70.467
1zgbA1EAcetylcholinesterase3.1.1.70.467
2bn4FMNNADPH--cytochrome P450 reductase/0.467
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.467
2xjc5GPCytosolic purine 5'-nucleotidase3.1.3.50.467
1r5hAO2Methionine aminopeptidase 2/0.465
1qtiGNTAcetylcholinesterase3.1.1.70.464
2ea4F79Methionine aminopeptidase 2/0.464
3dr7GPDGDP-perosamine synthase/0.464
2xufTZ4Acetylcholinesterase3.1.1.70.463
1r58AO5Methionine aminopeptidase 2/0.462
2g263LGRenin3.4.23.150.462
2xuhTZ4Acetylcholinesterase3.1.1.70.462
3h7rNAPAldo-keto reductase family 4 member C8/0.462
3ojwFMNNADPH--cytochrome P450 reductase/0.462
1i9c5ADGlutamate mutase epsilon subunit/0.461
2jf0HBPAcetylcholinesterase3.1.1.70.461
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.461
4d2dALA_ALA_ALADi-or tripeptide:H+ symporter/0.461
1dx6GNTAcetylcholinesterase3.1.1.70.460
1obnASVIsopenicillin N synthase1.21.3.10.460
1w6rGNTAcetylcholinesterase3.1.1.70.460
2cekN8TAcetylcholinesterase3.1.1.70.460
2wwjY28Lysine-specific demethylase 4A/0.460
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.460
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.460
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.460
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.459
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2aouCQAHistamine N-methyltransferase2.1.1.80.459
2bf4FMNNADPH--cytochrome P450 reductase/0.459
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.459
3qj0QI3Botulinum neurotoxin type A3.4.24.690.459
3v0o4GWHisto-blood group ABO system transferase/0.459
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.459
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.459
1q83TZ5Acetylcholinesterase3.1.1.70.458
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.458
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.458
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.458
4arbC57Acetylcholinesterase3.1.1.70.458
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.457
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.457
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
1w76GNTAcetylcholinesterase3.1.1.70.456
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.456
2yyeAPCSelenide, water dikinase2.7.9.30.456
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.456
3qeoLLTDeoxycytidine kinase2.7.1.740.456
3vilSA0Beta-glucosidase/0.456
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.455
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.455
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.455
3fhxPLPPyridoxal kinase2.7.1.350.455
4d6qPD2Lysine-specific demethylase 4D1.14.110.455
4kl1PCGPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.455
1mxfMTXPutative pteridine reductase 2/0.454
2xujTZ5Acetylcholinesterase3.1.1.70.454
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4to5DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.454
1esmCOAPantothenate kinase2.7.1.330.453
1h60STRPentaerythritol tetranitrate reductase/0.453
1q23FUAChloramphenicol acetyltransferase2.3.1.280.453
5ah5LSSLeucine--tRNA ligase/0.453
2oz57XYUncharacterized protein/0.452
3g70A5TRenin3.4.23.150.452
3nx2FERFerulic acid decarboxylase/0.452
3qfrFMNNADPH--cytochrome P450 reductase/0.452
4ey7E20Acetylcholinesterase3.1.1.70.452
4fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
4fapARDSerine/threonine-protein kinase mTOR2.7.11.10.452
1j37X8ZAngiotensin-converting enzyme3.4.15.10.451
1qpf858Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.451
1t7o152Carnitine O-acetyltransferase2.3.1.70.451
1vhzAPRADP compounds hydrolase NudE3.6.10.451
2fs4PZ1Renin3.4.23.150.451
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.451
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3pdqKC6Lysine-specific demethylase 4A1.14.110.451
3v0p4GWHisto-blood group ABO system transferase/0.451
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.451
1a7xFKAPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.450
2bf4FADNADPH--cytochrome P450 reductase/0.450
2il2LIXRenin3.4.23.150.450
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
2geuCOKPantothenate kinase2.7.1.330.449
2whqHI6Acetylcholinesterase3.1.1.70.449
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3h0bB35Beta-secretase 13.4.23.460.449
3h3qH13Collagen type IV alpha-3-binding protein/0.449
3intGDUUDP-galactopyranose mutase5.4.99.90.449
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.449
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
4to3DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1fxuGU7Purine nucleoside phosphorylase2.4.2.10.448
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.448
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.448
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.448
4nv1TYDFormyl transferase/0.448
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.447
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.447
2b58COADiamine acetyltransferase 1/0.447
2ckmAA7Acetylcholinesterase3.1.1.70.447
2vbqBSJAminoglycoside N(6')-acetyltransferase type 1/0.447
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.447
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.447
1fkgSB3Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
2xuiTZ5Acetylcholinesterase3.1.1.70.446
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.446
3qe2FMNNADPH--cytochrome P450 reductase/0.446
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.445
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.445
1ut6A8NAcetylcholinesterase3.1.1.70.445
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.445
2lfoGCHFatty acid-binding protein, liver/0.445
4bb2STRCorticosteroid-binding globulin/0.445
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.445
1bl4AP1Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
1gaxVAAValine--tRNA ligase6.1.1.90.444
3b4p3B4Phenazine biosynthesis protein A/B/0.444
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3q9bB3NAcetylpolyamine amidohydrolase/0.444
4b66NAPL-ornithine N(5)-monooxygenase/0.444
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.444
4q7f3D1Uncharacterized protein/0.444
2aovC2MHistamine N-methyltransferase2.1.1.80.443
2cdaNAPGlucose 1-dehydrogenase/0.443
2g1o2IGRenin3.4.23.150.443
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.443
3ha5SFGHydroxymycolate synthase MmaA42.1.10.443
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.443
3vjkM51Dipeptidyl peptidase 4/0.443
4j4nD44Peptidylprolyl isomerase/0.443
4jbsP52Endoplasmic reticulum aminopeptidase 23.4.110.443
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
1vkgCRIHistone deacetylase 83.5.1.980.442
2v16C47Renin3.4.23.150.442
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.442
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3wqmB29Diterpene synthase3.1.7.80.442
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.442
4nv10FXFormyl transferase/0.442
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
1h66RH1NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1tllFMNNitric oxide synthase, brain1.14.13.390.441
1u1cBAUUridine phosphorylase2.4.2.30.441
2abaSTRPentaerythritol tetranitrate reductase/0.441
2g1s4IGRenin3.4.23.150.441
2g1y5IGRenin3.4.23.150.441
3af0GDPPantothenate kinase2.7.1.330.441
3ivcFG4Pantothenate synthetase6.3.2.10.441
3mauEXTPutative sphingosine-1-phosphate lyase/0.441
4a83DXCMajor pollen allergen Bet v 1-A/0.441
4bftZVTPantothenate kinase2.7.1.330.441
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.441
1fkfFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.440
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3g72A6TRenin3.4.23.150.440
4bis8HQLysine-specific demethylase 4A1.14.110.440
4zwpM44Xaa-Pro dipeptidase3.4.13.90.440
5c1mCLRMu-type opioid receptor/0.440
5f8eSAHPossible transcriptional regulatory protein/0.440