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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
3pkbY16Methionine aminopeptidase 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3pkbY16Methionine aminopeptidase 2/1.000
3pkdY10Methionine aminopeptidase 2/0.680
3pkaY02Methionine aminopeptidase 2/0.657
3pkeY10Methionine aminopeptidase 2/0.647
4flkY10Methionine aminopeptidase 1/0.568
4fllYZ6Methionine aminopeptidase 1/0.562
4fliY16Methionine aminopeptidase 1/0.554
2nq7HM5Methionine aminopeptidase 1/0.543
3iu7FCDMethionine aminopeptidase 2/0.530
1r5gAO1Methionine aminopeptidase 2/0.527
2gg8U15Methionine aminopeptidase/0.525
3iu8T03Methionine aminopeptidase 2/0.525
2g6pHM2Methionine aminopeptidase 1/0.522
2evcFC3Methionine aminopeptidase/0.521
4iksTFDMethionine aminopeptidase 1/0.520
4iktTFVMethionine aminopeptidase 1/0.518
3iu9T07Methionine aminopeptidase 2/0.512
4fljY08Methionine aminopeptidase 1/0.507
4ikrPVPMethionine aminopeptidase 1/0.506
1r5hAO2Methionine aminopeptidase 2/0.500
2evmFC2Methionine aminopeptidase/0.500
1qzyTDEMethionine aminopeptidase 2/0.499
2ggbU17Methionine aminopeptidase/0.497
2q94A04Methionine aminopeptidase/0.491
4ikuSHXMethionine aminopeptidase 1/0.491
4hxx1AYMethionine aminopeptidase 1/0.485
3pkcY08Methionine aminopeptidase 2/0.481
1eveE20Acetylcholinesterase3.1.1.70.480
2q92B23Methionine aminopeptidase/0.479
1r58AO5Methionine aminopeptidase 2/0.475
2gg3U13Methionine aminopeptidase/0.474
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
2p99YE6Methionine aminopeptidase/0.472
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.471
4bftZVTPantothenate kinase2.7.1.330.470
1yw8A75Methionine aminopeptidase 2/0.467
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.466
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.466
2gg0U11Methionine aminopeptidase/0.466
5irnADPNucleotide binding oligomerization domain containing 2/0.464
2ea2F77Methionine aminopeptidase 2/0.463
2q93B21Methionine aminopeptidase/0.463
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
4nv10FXFormyl transferase/0.462
1ja0FMNNADPH--cytochrome P450 reductase/0.461
3d27W29Methionine aminopeptidase/0.461
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.460
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.459
3ojwFMNNADPH--cytochrome P450 reductase/0.459
3wqmB29Diterpene synthase3.1.7.80.457
2q96A18Methionine aminopeptidase/0.456
2xugTZ4Acetylcholinesterase3.1.1.70.456
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
2g247IGRenin3.4.23.150.454
1amoFMNNADPH--cytochrome P450 reductase/0.453
2ea4F79Methionine aminopeptidase 2/0.453
3ufl508Beta-secretase 13.4.23.460.453
4arbC57Acetylcholinesterase3.1.1.70.453
2p98YE7Methionine aminopeptidase/0.452
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
1odcA8BAcetylcholinesterase3.1.1.70.451
2g1n1IGRenin3.4.23.150.451
2ga2A19Methionine aminopeptidase 2/0.451
2gg2U12Methionine aminopeptidase/0.451
2j3qTFLAcetylcholinesterase3.1.1.70.451
2xukTZ5Acetylcholinesterase3.1.1.70.451
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.451
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.451
1q84TZ4Acetylcholinesterase3.1.1.70.450
1yw9A84Methionine aminopeptidase 2/0.450
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
3akn11DFatty acid-binding protein, intestinal/0.450
3f6sFMNFlavodoxin/0.450
1ja1FMNNADPH--cytochrome P450 reductase/0.449
2g226IGRenin3.4.23.150.449
4bfxZVXPantothenate kinase2.7.1.330.449
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1xnzFCDMethionine aminopeptidase/0.448
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.448
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.448
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.448
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.448
1h60STRPentaerythritol tetranitrate reductase/0.447
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.447
2xuqTZ4Acetylcholinesterase3.1.1.70.447
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.446
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.446
2whqHI6Acetylcholinesterase3.1.1.70.446
2wzySQXSoluble acetylcholine receptor/0.446
3f90FMNFlavodoxin/0.446
3qfrFMNNADPH--cytochrome P450 reductase/0.446
1ex75GPGuanylate kinase2.7.4.80.445
2gywOBIAcetylcholinesterase3.1.1.70.445
2ikuLIYRenin3.4.23.150.445
3qe2FMNNADPH--cytochrome P450 reductase/0.445
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
2x91LPRAngiotensin-converting enzyme3.4.15.10.444
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.444
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.443
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.443
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.443
2xuhTZ4Acetylcholinesterase3.1.1.70.443
2xupTZ5Acetylcholinesterase3.1.1.70.443
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4mlp2CXCryptochrome-2/0.443
4psbGA3Cytokinin-specific binding protein/0.443
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.442
2oz57XYUncharacterized protein/0.442
2wwjY28Lysine-specific demethylase 4A/0.442
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4b68FADL-ornithine N(5)-monooxygenase/0.442
4bfvZVVPantothenate kinase2.7.1.330.442
4m0f1YKAcetylcholinesterase3.1.1.70.442
1c7oPPGHemolysin/0.441
1qiqACCIsopenicillin N synthase1.21.3.10.441
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2qimZEAClass 10 plant pathogenesis-related protein/0.441
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.441
4b7zQ4QAcetylcholinesterase3.1.1.70.441
2eixFADNADH-cytochrome b5 reductase/0.440
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.440
2g1y5IGRenin3.4.23.150.440
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3hmvHBTcAMP-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
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.440