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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
2gg0U11Methionine aminopeptidase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2gg0U11Methionine aminopeptidase/1.000
2ggbU17Methionine aminopeptidase/0.673
2gg9U16Methionine aminopeptidase/0.654
2gg3U13Methionine aminopeptidase/0.645
2evcFC3Methionine aminopeptidase/0.620
2gg8U15Methionine aminopeptidase/0.614
2q93B21Methionine aminopeptidase/0.611
2p98YE7Methionine aminopeptidase/0.608
2q92B23Methionine aminopeptidase/0.608
3iu8T03Methionine aminopeptidase 2/0.607
2evmFC2Methionine aminopeptidase/0.606
2p99YE6Methionine aminopeptidase/0.606
2q96A18Methionine aminopeptidase/0.605
3pkeY10Methionine aminopeptidase 2/0.604
2gg2U12Methionine aminopeptidase/0.597
3iu7FCDMethionine aminopeptidase 2/0.596
4iktTFVMethionine aminopeptidase 1/0.594
2q94A04Methionine aminopeptidase/0.591
1c23MPHMethionine aminopeptidase/0.574
3d27W29Methionine aminopeptidase/0.574
3pkdY10Methionine aminopeptidase 2/0.565
4ikuSHXMethionine aminopeptidase 1/0.562
4iksTFDMethionine aminopeptidase 1/0.541
4hxx1AYMethionine aminopeptidase 1/0.538
4flkY10Methionine aminopeptidase 1/0.537
1xnzFCDMethionine aminopeptidase/0.535
3pkbY16Methionine aminopeptidase 2/0.532
3pkcY08Methionine aminopeptidase 2/0.531
2nq7HM5Methionine aminopeptidase 1/0.526
3pkaY02Methionine aminopeptidase 2/0.526
4ikrPVPMethionine aminopeptidase 1/0.518
4fllYZ6Methionine aminopeptidase 1/0.517
4fliY16Methionine aminopeptidase 1/0.514
4fljY08Methionine aminopeptidase 1/0.511
1r5gAO1Methionine aminopeptidase 2/0.504
2oazI96Methionine aminopeptidase 2/0.498
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.498
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.489
2wzySQXSoluble acetylcholine receptor/0.488
4m0f1YKAcetylcholinesterase3.1.1.70.488
2gywOBIAcetylcholinesterase3.1.1.70.485
1odcA8BAcetylcholinesterase3.1.1.70.483
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.483
4b7zQ4QAcetylcholinesterase3.1.1.70.483
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.483
2cekN8TAcetylcholinesterase3.1.1.70.482
3pdqKC6Lysine-specific demethylase 4A1.14.110.479
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.478
1q84TZ4Acetylcholinesterase3.1.1.70.477
2xuoTZ4Acetylcholinesterase3.1.1.70.477
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.475
1eveE20Acetylcholinesterase3.1.1.70.474
1r58AO5Methionine aminopeptidase 2/0.474
1lc3NADBiliverdin reductase A1.3.1.240.473
1qzyTDEMethionine aminopeptidase 2/0.473
1yw7A41Methionine aminopeptidase 2/0.473
2ga2A19Methionine aminopeptidase 2/0.473
2whqHI6Acetylcholinesterase3.1.1.70.472
4bfxZVXPantothenate kinase2.7.1.330.472
2xukTZ5Acetylcholinesterase3.1.1.70.471
4ey6GNTAcetylcholinesterase3.1.1.70.471
2xujTZ5Acetylcholinesterase3.1.1.70.470
2xupTZ5Acetylcholinesterase3.1.1.70.470
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.470
1zgbA1EAcetylcholinesterase3.1.1.70.469
2ha6SCKAcetylcholinesterase3.1.1.70.468
2pb1NFGGlucan 1,3-beta-glucosidase/0.468
1e6zNGOChitinase/0.467
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.467
2vd7PD2Lysine-specific demethylase 4A1.14.110.466
2w6cBM4Acetylcholinesterase3.1.1.70.466
3tdvGDPGentamicin resistance protein/0.466
2xuhTZ4Acetylcholinesterase3.1.1.70.465
2ea4F79Methionine aminopeptidase 2/0.464
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.464
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.464
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.463
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.463
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.463
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.463
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.462
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.462
2wcgMT5Glucosylceramidase3.2.1.450.462
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.462
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
1e66HUXAcetylcholinesterase3.1.1.70.461
2jf0HBPAcetylcholinesterase3.1.1.70.461
2jl1NAPTriphenylmethane reductase/0.461
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.461
2xugTZ4Acetylcholinesterase3.1.1.70.461
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.461
4gd40WSLysine-specific demethylase 4A1.14.110.460
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.459
3t0iSAHPutative methyltransferase/0.459
1x1bSAHC-20 methyltransferase/0.458
2g6pHM2Methionine aminopeptidase 1/0.458
2xuiTZ5Acetylcholinesterase3.1.1.70.457
3b1dPLSBetaC-S lyase/0.457
3rsv3RSBeta-secretase 13.4.23.460.457
2j3qTFLAcetylcholinesterase3.1.1.70.456
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.455
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.455
1x1aSAMC-20 methyltransferase/0.455
1yw9A84Methionine aminopeptidase 2/0.455
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
2xufTZ4Acetylcholinesterase3.1.1.70.455
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.455
3d91REMRenin3.4.23.150.455
3qj0QI3Botulinum neurotoxin type A3.4.24.690.455
3vetADPnebramycin 5' synthase6.1.2.20.455
3sxjSAMPutative methyltransferase/0.454
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.454
3wqmB29Diterpene synthase3.1.7.80.454
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.454
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.453
1vkgCRIHistone deacetylase 83.5.1.980.453
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.453
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.453
4fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.453
4fapARDSerine/threonine-protein kinase mTOR2.7.11.10.453
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.452
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.452
2hxzH7JCathepsin S3.4.22.270.452
2wvmGDDMannosyl-3-phosphogylcerate synthase/0.452
3iu9T07Methionine aminopeptidase 2/0.452
4arbC57Acetylcholinesterase3.1.1.70.452
4zwpM44Xaa-Pro dipeptidase3.4.13.90.452
1yw8A75Methionine aminopeptidase 2/0.451
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.451
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.451
5jy1NADPutative short-chain dehydrogenase/reductase/0.451
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
1zgcA2EAcetylcholinesterase3.1.1.70.450
2aouCQAHistamine N-methyltransferase2.1.1.80.450
2g1s4IGRenin3.4.23.150.450
2v34CTN4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.450
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.450
3rvhHQ2Lysine-specific demethylase 4A1.14.110.450
4nv14TGFormyl transferase/0.450
4nv10FXFormyl transferase/0.450
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.449
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2zsaADPPantothenate kinase2.7.1.330.449
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.449
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
4ey7E20Acetylcholinesterase3.1.1.70.449
1p0pBCHCholinesterase3.1.1.80.448
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.448
1w4lGL8Acetylcholinesterase3.1.1.70.448
2getCOKPantothenate kinase2.7.1.330.448
2gs9SAHUncharacterized protein/0.448
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
3wi2P98cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.448
1dx6GNTAcetylcholinesterase3.1.1.70.447
1h22E10Acetylcholinesterase3.1.1.70.447
1i9c5ADGlutamate mutase epsilon subunit/0.447
1nhkCMPNucleoside diphosphate kinase2.7.4.60.447
1w6rGNTAcetylcholinesterase3.1.1.70.447
2ea2F77Methionine aminopeptidase 2/0.447
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.447
3rthRTHBeta-secretase 13.4.23.460.447
2ct8MSPMethionine--tRNA ligase6.1.1.100.446
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.446
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.446
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.446
3n14FMNXenobiotic reductase/0.446
3ziuLSSLeucyl-tRNA synthetase/0.446
4q7f3D1Uncharacterized protein/0.446
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.445
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.445
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
3aezGDPPantothenate kinase2.7.1.330.445
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.445
3rtnRTNBeta-secretase 13.4.23.460.445
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.445
1r5hAO2Methionine aminopeptidase 2/0.444
2ab8MTPAdenosine kinase2.7.1.200.444
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.444
2v8pCDP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.444
3ha5SFGHydroxymycolate synthase MmaA42.1.10.444
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.444
1esmCOAPantothenate kinase2.7.1.330.443
1u1gBBBUridine phosphorylase2.4.2.30.443
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3af4GCPPantothenate kinase2.7.1.330.443
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.443
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.443
3h3qH13Collagen type IV alpha-3-binding protein/0.443
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.442
2a9y26AAdenosine kinase2.7.1.200.442
2b58COADiamine acetyltransferase 1/0.442
2qimZEAClass 10 plant pathogenesis-related protein/0.442
3apwDP0Alpha-1-acid glycoprotein 2/0.442
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3zv7NHGAcetylcholinesterase3.1.1.70.442
5fmmMGTPolymerase basic protein 2/0.442
7req2CPMethylmalonyl-CoA mutase large subunit5.4.99.20.442
1g6kNADGlucose 1-dehydrogenase1.1.1.470.441
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.441
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.441
1ry8RUTAldo-keto reductase family 1 member C3/0.441
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.441
4b79NADProbable short-chain dehydrogenase/0.441
4n3r2GUTankyrase-12.4.2.300.441
1kw0H4BPhenylalanine-4-hydroxylase1.14.16.10.440
1u65CP0Acetylcholinesterase3.1.1.70.440
2a3bCFFEndochitinase B13.2.1.140.440
2b3dFADModulator of drug activity B/0.440
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2g1n1IGRenin3.4.23.150.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.440
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2zsbADPPantothenate kinase2.7.1.330.440
3af2ACPPantothenate kinase2.7.1.330.440
3d64NADAdenosylhomocysteinase/0.440
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.440
3tqcADPPantothenate kinase/0.440
3vf2ADPnebramycin 5' synthase6.1.2.20.440
4araC56Acetylcholinesterase3.1.1.70.440
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.440
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4fhd0TTSpore photoproduct lyase/0.440