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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
4fliY16Methionine aminopeptidase 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4fliY16Methionine aminopeptidase 1/1.000
4iktTFVMethionine aminopeptidase 1/0.739
4ikuSHXMethionine aminopeptidase 1/0.707
4ikrPVPMethionine aminopeptidase 1/0.684
4flkY10Methionine aminopeptidase 1/0.671
4fllYZ6Methionine aminopeptidase 1/0.668
4fljY08Methionine aminopeptidase 1/0.661
4hxx1AYMethionine aminopeptidase 1/0.652
3pkeY10Methionine aminopeptidase 2/0.647
3pkaY02Methionine aminopeptidase 2/0.646
3pkdY10Methionine aminopeptidase 2/0.646
2evcFC3Methionine aminopeptidase/0.628
3pkbY16Methionine aminopeptidase 2/0.625
3iu7FCDMethionine aminopeptidase 2/0.623
1c23MPHMethionine aminopeptidase/0.622
2evmFC2Methionine aminopeptidase/0.614
3iu8T03Methionine aminopeptidase 2/0.608
3pkcY08Methionine aminopeptidase 2/0.602
2q92B23Methionine aminopeptidase/0.598
2q93B21Methionine aminopeptidase/0.596
2g6pHM2Methionine aminopeptidase 1/0.595
2nq7HM5Methionine aminopeptidase 1/0.591
2gg8U15Methionine aminopeptidase/0.586
2q96A18Methionine aminopeptidase/0.583
4iksTFDMethionine aminopeptidase 1/0.580
2q94A04Methionine aminopeptidase/0.579
1r5gAO1Methionine aminopeptidase 2/0.573
2ggbU17Methionine aminopeptidase/0.569
2gg3U13Methionine aminopeptidase/0.556
3d27W29Methionine aminopeptidase/0.551
2gg0U11Methionine aminopeptidase/0.545
2p98YE7Methionine aminopeptidase/0.527
1xnzFCDMethionine aminopeptidase/0.525
2ga2A19Methionine aminopeptidase 2/0.523
2p99YE6Methionine aminopeptidase/0.522
2gg9U16Methionine aminopeptidase/0.519
2ea2F77Methionine aminopeptidase 2/0.518
1r5hAO2Methionine aminopeptidase 2/0.517
1r58AO5Methionine aminopeptidase 2/0.504
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.501
1yw8A75Methionine aminopeptidase 2/0.498
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.498
2ea4F79Methionine aminopeptidase 2/0.497
1q84TZ4Acetylcholinesterase3.1.1.70.496
1yw9A84Methionine aminopeptidase 2/0.496
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.496
3iu9T07Methionine aminopeptidase 2/0.494
1qzyTDEMethionine aminopeptidase 2/0.493
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.490
1h60STRPentaerythritol tetranitrate reductase/0.485
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.484
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.483
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.482
4gd40WSLysine-specific demethylase 4A1.14.110.481
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.480
2oazI96Methionine aminopeptidase 2/0.480
2xugTZ4Acetylcholinesterase3.1.1.70.480
2jf0HBPAcetylcholinesterase3.1.1.70.478
2w6cBM4Acetylcholinesterase3.1.1.70.477
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.477
3rvhHQ2Lysine-specific demethylase 4A1.14.110.477
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.476
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.475
2gg2U12Methionine aminopeptidase/0.475
2xupTZ5Acetylcholinesterase3.1.1.70.475
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.475
3q43D66M1 family aminopeptidase3.4.110.475
3h0bB35Beta-secretase 13.4.23.460.474
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.474
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.474
2whqHI6Acetylcholinesterase3.1.1.70.473
3v0o4GWHisto-blood group ABO system transferase/0.473
4lutDCSAlanine racemase/0.472
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.471
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.471
2ckmAA7Acetylcholinesterase3.1.1.70.471
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.471
1ex75GPGuanylate kinase2.7.4.80.470
4ey6GNTAcetylcholinesterase3.1.1.70.470
2cekN8TAcetylcholinesterase3.1.1.70.469
2ct8MSPMethionine--tRNA ligase6.1.1.100.469
2vd7PD2Lysine-specific demethylase 4A1.14.110.469
4ey7E20Acetylcholinesterase3.1.1.70.469
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.468
2j3qTFLAcetylcholinesterase3.1.1.70.468
2xukTZ5Acetylcholinesterase3.1.1.70.468
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.468
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.468
1gaxVAAValine--tRNA ligase6.1.1.90.467
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.466
1vkgCRIHistone deacetylase 83.5.1.980.466
2aouCQAHistamine N-methyltransferase2.1.1.80.466
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.466
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.466
1odcA8BAcetylcholinesterase3.1.1.70.465
2xuoTZ4Acetylcholinesterase3.1.1.70.465
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4m0f1YKAcetylcholinesterase3.1.1.70.465
1h22E10Acetylcholinesterase3.1.1.70.464
2gv8NDPThiol-specific monooxygenase1.14.130.464
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.463
1qtiGNTAcetylcholinesterase3.1.1.70.463
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3mauPLRPutative sphingosine-1-phosphate lyase/0.463
2oz57XYUncharacterized protein/0.462
2rqfJH3Hemolymph juvenile hormone binding protein/0.462
2wzySQXSoluble acetylcholine receptor/0.462
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3mauEXTPutative sphingosine-1-phosphate lyase/0.462
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.462
2jl1NAPTriphenylmethane reductase/0.461
2pncCLUPrimary amine oxidase, liver isozyme/0.461
4j0v1H7Beta-secretase 13.4.23.460.461
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.460
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3h3qH13Collagen type IV alpha-3-binding protein/0.460
3wqmB29Diterpene synthase3.1.7.80.460
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.460
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.459
2qimZEAClass 10 plant pathogenesis-related protein/0.459
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.459
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.459
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.459
1w6rGNTAcetylcholinesterase3.1.1.70.458
3pdqKC6Lysine-specific demethylase 4A1.14.110.458
4araC56Acetylcholinesterase3.1.1.70.458
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.458
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.458
1w76GNTAcetylcholinesterase3.1.1.70.457
1xddAAYIntegrin alpha-L/0.457
2g1y5IGRenin3.4.23.150.457
2xujTZ5Acetylcholinesterase3.1.1.70.457
3i0oSMISpectinomycin phosphotransferase/0.457
3mjrAC2Deoxycytidine kinase2.7.1.740.457
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.457
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.456
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.456
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.456
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3vilSA0Beta-glucosidase/0.456
4b7zQ4QAcetylcholinesterase3.1.1.70.456
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
1eveE20Acetylcholinesterase3.1.1.70.455
2aot2PMHistamine N-methyltransferase2.1.1.80.455
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.455
1yw7A41Methionine aminopeptidase 2/0.454
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3ufl508Beta-secretase 13.4.23.460.454
3w3nRX8Toll-like receptor 8/0.454
4arbC57Acetylcholinesterase3.1.1.70.454
4gddNAIUDP-galactopyranose mutase/0.454
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.454
2bf4FADNADPH--cytochrome P450 reductase/0.453
2xuqTZ4Acetylcholinesterase3.1.1.70.453
2zsbADPPantothenate kinase2.7.1.330.453
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
4azaMGOEukaryotic translation initiation factor 4E/0.453
4lh71X8DNA ligase/0.453
2gywOBIAcetylcholinesterase3.1.1.70.452
4dh0MR8Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
1gky5GPGuanylate kinase2.7.4.80.451
2g1o2IGRenin3.4.23.150.451
2pb1NFGGlucan 1,3-beta-glucosidase/0.451
2xufTZ4Acetylcholinesterase3.1.1.70.451
3af1GDPPantothenate kinase2.7.1.330.451
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.451
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.451
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.451
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.451
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.451
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4nv10FXFormyl transferase/0.451
3uonQNBMuscarinic acetylcholine receptor M2/0.451
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2ha6SCKAcetylcholinesterase3.1.1.70.450
3ccc7ACDipeptidyl peptidase 4/0.450
3fktSIIBeta-secretase 13.4.23.460.450
4bfwZVWPantothenate kinase2.7.1.330.450
4bis8HQLysine-specific demethylase 4A1.14.110.450
1amoFMNNADPH--cytochrome P450 reductase/0.449
3akn11DFatty acid-binding protein, intestinal/0.449
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.449
3vjkM51Dipeptidyl peptidase 4/0.449
1amoNAPNADPH--cytochrome P450 reductase/0.448
1t7o152Carnitine O-acetyltransferase2.3.1.70.448
1zgbA1EAcetylcholinesterase3.1.1.70.448
2c6c24IGlutamate carboxypeptidase 23.4.17.210.448
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.448
3b6pTMPThree-prime repair exonuclease 13.1.11.20.448
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4b63NAPL-ornithine N(5)-monooxygenase/0.448
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4rxpDTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
4zwpM44Xaa-Pro dipeptidase3.4.13.90.448
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1zgcA2EAcetylcholinesterase3.1.1.70.447
2c20NADUDP-glucose 4-epimerase/0.447
3aezGDPPantothenate kinase2.7.1.330.447
3n87N873-dehydroquinate dehydratase4.2.1.100.447
3v2uATPProtein GAL3/0.447
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.447
4j4nD44Peptidylprolyl isomerase/0.447
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.447
1dx6GNTAcetylcholinesterase3.1.1.70.446
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.446
1ut6A8NAcetylcholinesterase3.1.1.70.446
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3ziuLSSLeucyl-tRNA synthetase/0.446
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.445
3dz6M8ES-adenosylmethionine decarboxylase proenzyme4.1.1.500.445
3mj4URMUDP-galactopyranose mutase/0.445
4b66NAPL-ornithine N(5)-monooxygenase/0.445
4bftZVTPantothenate kinase2.7.1.330.445
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.445
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.445
5ah5LSSLeucine--tRNA ligase/0.445
2g1s4IGRenin3.4.23.150.444
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3g0bT22Dipeptidyl peptidase 4/0.444
3g0gRUMDipeptidyl peptidase 4/0.444
3rsv3RSBeta-secretase 13.4.23.460.444
1kwcBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.443
2a4xBLMMitomycin-binding protein/0.443
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.443
2dg4RAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
2ejzSAHDiphthine synthase/0.443
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2xlpNAPPutative flavin-containing monooxygenase/0.443
2xuhTZ4Acetylcholinesterase3.1.1.70.443
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3o5rFK5Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.443
4b63FADL-ornithine N(5)-monooxygenase/0.443
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
4psbGA3Cytokinin-specific binding protein/0.443
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor/0.442
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.442
2g247IGRenin3.4.23.150.442
2il2LIXRenin3.4.23.150.442
2rlcCHDCholoylglycine hydrolase3.5.1.240.442
2xnvVU3Soluble acetylcholine receptor/0.442
3skgPB8Beta-secretase 13.4.23.460.442
3v0p4GWHisto-blood group ABO system transferase/0.442
4e2yJHZMethyltransferase/0.442
4eb5PLPCysteine desulfurase IscS 2/0.442
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1qpf858Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
2aovC2MHistamine N-methyltransferase2.1.1.80.441
2g1n1IGRenin3.4.23.150.441
2hpvFMNFMN-dependent NADH-azoreductase1.70.441
2wwjY28Lysine-specific demethylase 4A/0.441
2xuiTZ5Acetylcholinesterase3.1.1.70.441
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
2z4w749Geranylgeranyl pyrophosphate synthase/0.441
3hiiPNTAmiloride-sensitive amine oxidase [copper-containing]/0.441
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4b64NAPL-ornithine N(5)-monooxygenase/0.441
1a4wQWEProthrombin3.4.21.50.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2g21L1BRenin3.4.23.150.440
2i4qUA4Renin3.4.23.150.440
3f8sPF2Dipeptidyl peptidase 4/0.440
3h2sNDPPutative NADH-flavin reductase/0.440
3kkzSAMUncharacterized protein/0.440
4bb2STRCorticosteroid-binding globulin/0.440
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.440