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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4ikuSHXMethionine aminopeptidase 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4ikuSHXMethionine aminopeptidase 1/1.000
4ikrPVPMethionine aminopeptidase 1/0.813
4iktTFVMethionine aminopeptidase 1/0.752
4fliY16Methionine aminopeptidase 1/0.721
3pkeY10Methionine aminopeptidase 2/0.656
1c23MPHMethionine aminopeptidase/0.644
3iu8T03Methionine aminopeptidase 2/0.639
2gg0U11Methionine aminopeptidase/0.624
2nq7HM5Methionine aminopeptidase 1/0.624
2gg8U15Methionine aminopeptidase/0.623
2evcFC3Methionine aminopeptidase/0.622
4hxx1AYMethionine aminopeptidase 1/0.621
2g6pHM2Methionine aminopeptidase 1/0.615
3pkdY10Methionine aminopeptidase 2/0.615
2ggbU17Methionine aminopeptidase/0.611
3iu7FCDMethionine aminopeptidase 2/0.610
4iksTFDMethionine aminopeptidase 1/0.606
2evmFC2Methionine aminopeptidase/0.602
3pkaY02Methionine aminopeptidase 2/0.601
2p99YE6Methionine aminopeptidase/0.600
2q92B23Methionine aminopeptidase/0.600
2gg3U13Methionine aminopeptidase/0.597
4fllYZ6Methionine aminopeptidase 1/0.596
4flkY10Methionine aminopeptidase 1/0.583
2q93B21Methionine aminopeptidase/0.573
3pkbY16Methionine aminopeptidase 2/0.572
2q94A04Methionine aminopeptidase/0.564
3d27W29Methionine aminopeptidase/0.563
1xnzFCDMethionine aminopeptidase/0.560
2q96A18Methionine aminopeptidase/0.560
2gg9U16Methionine aminopeptidase/0.554
3pkcY08Methionine aminopeptidase 2/0.547
3iu9T07Methionine aminopeptidase 2/0.545
2gg2U12Methionine aminopeptidase/0.543
2p98YE7Methionine aminopeptidase/0.540
2ga2A19Methionine aminopeptidase 2/0.521
2oazI96Methionine aminopeptidase 2/0.520
4fljY08Methionine aminopeptidase 1/0.519
1qzyTDEMethionine aminopeptidase 2/0.512
1r5gAO1Methionine aminopeptidase 2/0.508
1e6zNGOChitinase/0.506
1yw9A84Methionine aminopeptidase 2/0.504
1zgbA1EAcetylcholinesterase3.1.1.70.504
2j3qTFLAcetylcholinesterase3.1.1.70.504
2ea2F77Methionine aminopeptidase 2/0.501
1eveE20Acetylcholinesterase3.1.1.70.492
1dx6GNTAcetylcholinesterase3.1.1.70.490
1yw8A75Methionine aminopeptidase 2/0.486
1w6rGNTAcetylcholinesterase3.1.1.70.484
1odcA8BAcetylcholinesterase3.1.1.70.480
2ea4F79Methionine aminopeptidase 2/0.476
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.474
2xugTZ4Acetylcholinesterase3.1.1.70.473
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.471
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.470
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.470
2cekN8TAcetylcholinesterase3.1.1.70.469
4m0f1YKAcetylcholinesterase3.1.1.70.469
1zgcA2EAcetylcholinesterase3.1.1.70.468
1r5hAO2Methionine aminopeptidase 2/0.467
2xupTZ5Acetylcholinesterase3.1.1.70.467
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.467
3pdqKC6Lysine-specific demethylase 4A1.14.110.466
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
2xi4AFTAcetylcholinesterase3.1.1.70.465
1yw7A41Methionine aminopeptidase 2/0.464
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.464
2gywOBIAcetylcholinesterase3.1.1.70.464
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
4isuIKMGlutamate receptor 2/0.464
4zwpM44Xaa-Pro dipeptidase3.4.13.90.463
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
2xuhTZ4Acetylcholinesterase3.1.1.70.462
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.462
2fs4PZ1Renin3.4.23.150.460
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
2pb1NFGGlucan 1,3-beta-glucosidase/0.460
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.460
3rtnRTNBeta-secretase 13.4.23.460.459
5c1mCLRMu-type opioid receptor/0.459
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.458
4ey6GNTAcetylcholinesterase3.1.1.70.458
2vn1FK5Peptidylprolyl isomerase/0.457
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.457
1qtiGNTAcetylcholinesterase3.1.1.70.456
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.456
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.456
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.455
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.455
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.455
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.455
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.454
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
2xuqTZ4Acetylcholinesterase3.1.1.70.453
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.453
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2gs9SAHUncharacterized protein/0.452
2jf0HBPAcetylcholinesterase3.1.1.70.452
4arbC57Acetylcholinesterase3.1.1.70.452
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
2whqHI6Acetylcholinesterase3.1.1.70.451
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.451
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.451
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1esmCOAPantothenate kinase2.7.1.330.450
1q84TZ4Acetylcholinesterase3.1.1.70.450
4gtt7TQGeranylgeranyl transferase type-2 subunit beta2.5.1.600.450
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
1a26CNAPoly [ADP-ribose] polymerase 12.4.2.300.449
3h7rNAPAldo-keto reductase family 4 member C8/0.449
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.449
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.449
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.449
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.449
4req5ADMethylmalonyl-CoA mutase large subunit5.4.99.20.449
2xukTZ5Acetylcholinesterase3.1.1.70.448
2ct8MSPMethionine--tRNA ligase6.1.1.100.447
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
3d64NADAdenosylhomocysteinase/0.447
3rvhHQ2Lysine-specific demethylase 4A1.14.110.447
1sg0STLRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.446
1u08PLPMethionine aminotransferase/0.446
3aezGDPPantothenate kinase2.7.1.330.446
3ufl508Beta-secretase 13.4.23.460.446
4ey7E20Acetylcholinesterase3.1.1.70.446
2xujTZ5Acetylcholinesterase3.1.1.70.445
3apwDP0Alpha-1-acid glycoprotein 2/0.445
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.445
3zv7NHGAcetylcholinesterase3.1.1.70.445
1s07PLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.444
1x1bSAHC-20 methyltransferase/0.444
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.444
3v0m5GWHisto-blood group ABO system transferase/0.444
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4b7zQ4QAcetylcholinesterase3.1.1.70.443
1jwtBLIProthrombin3.4.21.50.442
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
1r58AO5Methionine aminopeptidase 2/0.442
3ox279XRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
1kruIPTGalactoside O-acetyltransferase2.3.1.180.441
1votHUPAcetylcholinesterase3.1.1.70.441
2a3bCFFEndochitinase B13.2.1.140.441
2fk8SAMHydroxymycolate synthase MmaA42.1.10.441
2iyaZIOOleandomycin glycosyltransferase/0.441
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.441
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.440
3djjFADGlutathione reductase, mitochondrial1.8.1.70.440
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.440