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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
3dz4C8MS-adenosylmethionine decarboxylase proenzyme4.1.1.50

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3dz4C8MS-adenosylmethionine decarboxylase proenzyme4.1.1.501.000
3dz2A8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.797
3dz6M8ES-adenosylmethionine decarboxylase proenzyme4.1.1.500.743
3h0wN8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.691
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.685
3h0vM2TS-adenosylmethionine decarboxylase proenzyme4.1.1.500.604
1i7mCGS-adenosylmethionine decarboxylase proenzyme4.1.1.500.568
1i7cMGBS-adenosylmethionine decarboxylase proenzyme4.1.1.500.554
2ejzSAHDiphthine synthase/0.521
2w6cBM4Acetylcholinesterase3.1.1.70.517
1u65CP0Acetylcholinesterase3.1.1.70.513
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.513
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.487
3otwCOAPhosphopantetheine adenylyltransferase/0.486
4arbC57Acetylcholinesterase3.1.1.70.486
1q84TZ4Acetylcholinesterase3.1.1.70.485
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.485
3qgf46FGenome polyprotein2.7.7.480.483
1eveE20Acetylcholinesterase3.1.1.70.482
2gjlFMNNitronate monooxygenase1.13.12.160.482
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.481
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.480
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.480
2zs9ADPPantothenate kinase2.7.1.330.480
2v57PRLTetR family transcriptional regulator/0.479
3zv7NHGAcetylcholinesterase3.1.1.70.479
1e66HUXAcetylcholinesterase3.1.1.70.477
4hmwFMNPyridoxamine 5'-phosphate oxidase/0.477
1x1aSAMC-20 methyltransferase/0.476
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.476
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.476
1votHUPAcetylcholinesterase3.1.1.70.475
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
4ey6GNTAcetylcholinesterase3.1.1.70.475
2j3qTFLAcetylcholinesterase3.1.1.70.473
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.473
4araC56Acetylcholinesterase3.1.1.70.473
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.472
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.472
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.472
1qtiGNTAcetylcholinesterase3.1.1.70.471
1w4lGL8Acetylcholinesterase3.1.1.70.471
2xuqTZ4Acetylcholinesterase3.1.1.70.471
4a81DXCMajor pollen allergen Bet v 1-A/0.471
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.470
1dx6GNTAcetylcholinesterase3.1.1.70.468
2xukTZ5Acetylcholinesterase3.1.1.70.468
3mauPLRPutative sphingosine-1-phosphate lyase/0.468
1h22E10Acetylcholinesterase3.1.1.70.467
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.467
4bprFADFerredoxin--NADP reductase1.18.1.20.467
4br3U85Choline kinase alpha2.7.1.320.467
1jdzFMBPurine nucleoside phosphorylase/0.466
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.466
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
1xf0ASDAldo-keto reductase family 1 member C3/0.465
1ygjRMCPyridoxal kinase2.7.1.350.465
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.464
4a862ANMajor pollen allergen Bet v 1-A/0.464
1fw0KAIGlutamate receptor 2/0.463
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.463
1ry8RUTAldo-keto reductase family 1 member C3/0.462
4ey7E20Acetylcholinesterase3.1.1.70.462
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.462
1ry0PG2Aldo-keto reductase family 1 member C3/0.461
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
2gyuHI6Acetylcholinesterase3.1.1.70.461
2zevIPEGeranylgeranyl pyrophosphate synthase/0.461
3e6eDCSAlanine racemase/0.461
3oafOAGDihydrofolate reductase1.5.1.30.461
3p0fBAUUridine phosphorylase 22.4.2.30.461
4a802ANMajor pollen allergen Bet v 1-A/0.461
4a86H35Major pollen allergen Bet v 1-A/0.461
1w6rGNTAcetylcholinesterase3.1.1.70.460
1zgbA1EAcetylcholinesterase3.1.1.70.460
2g8yNADHydroxycarboxylate dehydrogenase B/0.460
2xlpNAPPutative flavin-containing monooxygenase/0.460
2xupTZ5Acetylcholinesterase3.1.1.70.460
3af0GDPPantothenate kinase2.7.1.330.460
3c1oNAPEugenol synthase/0.460
4jtqFLPAldo-keto reductase family 1 member C2/0.460
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.460
4psbGA3Cytokinin-specific binding protein/0.460
1odcA8BAcetylcholinesterase3.1.1.70.459
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.459
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.459
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.459
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.459
4i101BSBeta-secretase 13.4.23.460.459
4m0f1YKAcetylcholinesterase3.1.1.70.459
5a4vQUEGlutathione S-transferase F22.5.1.180.459
3vf60H6Glucokinase2.7.1.20.458
4fx9COACoenzyme A disulfide reductase1.8.1.140.458
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.457
4gdcNDPUDP-galactopyranose mutase/0.457
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.457
4j7gTRHPCZA361.3/0.457
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.456
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.456
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.456
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.456
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.456
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.456
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.456
1t7o152Carnitine O-acetyltransferase2.3.1.70.455
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.455
2xufTZ4Acetylcholinesterase3.1.1.70.455
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4hhy15RPoly [ADP-ribose] polymerase 12.4.2.300.455
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.454
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.454
4b7zQ4QAcetylcholinesterase3.1.1.70.454
4e32DWNMethyltransferase/0.454
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1e6zNGOChitinase/0.453
1g63FMNEpidermin decarboxylase4.1.10.453
1psa0ZLPepsin A3.4.23.10.453
3aezGDPPantothenate kinase2.7.1.330.453
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.453
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.453
4p9dTMPDeoxycytidylate deaminase/0.453
1o9bNAIQuinate/shikimate dehydrogenase/0.452
1vbiNADMalate/L-lactate dehydrogenase family protein/0.452
2abaSTRPentaerythritol tetranitrate reductase/0.452
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3ndjJHZMethyltransferase/0.452
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.452
4relKMPGlycosyltransferase/0.452
1lc3NADBiliverdin reductase A1.3.1.240.451
1sm4FADFerredoxin--NADP reductase/0.451
2gywOBIAcetylcholinesterase3.1.1.70.451
3r43ID8Aldo-keto reductase family 1 member C3/0.451
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.451
1ut6A8NAcetylcholinesterase3.1.1.70.450
2wnbC5PCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 12.4.99.40.450
2xytTC9Soluble acetylcholine receptor/0.450
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.450
5a0112VO-glycosyltransferase/0.450
1s7gNADNAD-dependent protein deacylase 2/0.449
2fxuBIDActin, alpha skeletal muscle/0.449
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3zkyWT4Isopenicillin N synthase1.21.3.10.449
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.449
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.449
5ds309LPoly [ADP-ribose] polymerase 12.4.2.300.449
1xh5R68cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3ai0PNWBeta-glucosidase/0.448
3cb2GDPTubulin gamma-1 chain/0.448
3ck7ACXStarch-binding protein SusD/0.448
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.448
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.448
1q83TZ5Acetylcholinesterase3.1.1.70.447
2ckmAA7Acetylcholinesterase3.1.1.70.447
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.447
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.447
4frkDWDBeta-secretase 13.4.23.460.447
1odjGMPPurine nucleoside phosphorylase/0.446
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
1wkhPPE[LysW]-aminoadipate semialdehyde transaminase/0.446
2gesCOKPantothenate kinase2.7.1.330.446
2gpjFADSiderophore-interacting protein/0.446
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.446
2jl1NAPTriphenylmethane reductase/0.446
2ym2NAPPhenylacetone monooxygenase1.14.13.920.446
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.446
4wecNADShort chain dehydrogenase/0.446
5d5bCAUBeta-2 adrenergic receptor/0.446
1lnmDTXBilin-binding protein/0.445
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.445
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.445
2cnsACORibosomal-protein-alanine acetyltransferase/0.445
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.445
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.445
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.445
4f3gKAIGlutamate receptor 3/0.445
4l65C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.445
3uonQNBMuscarinic acetylcholine receptor M2/0.445
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.444
2j9lATPH(+)/Cl(-) exchange transporter 5/0.444
2wjoQUDBeta-secretase 13.4.23.460.444
2xnvVU3Soluble acetylcholine receptor/0.444
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.444
4hb9FADUncharacterized protein/0.444
4plpNADHomospermidine synthase2.5.1.440.444
1b2lNDCAlcohol dehydrogenase1.1.1.10.443
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.443
1xvaSAMGlycine N-methyltransferase2.1.1.200.443
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.443
2ha6SCKAcetylcholinesterase3.1.1.70.443
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.443
2xujTZ5Acetylcholinesterase3.1.1.70.443
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3rsv3RSBeta-secretase 13.4.23.460.443
3w4k3LDD-amino-acid oxidase1.4.3.30.443
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.443
4bgg844Activin receptor type-12.7.11.300.443
4dch4DCGlucokinase2.7.1.20.443
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.443
5ah5LSSLeucine--tRNA ligase/0.443
1qoqIGPTryptophan synthase alpha chain/0.442
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.442
2b99RDLRiboflavin synthase2.5.1.90.442
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2weaPP6Penicillopepsin-13.4.23.200.442
2y1w849Histone-arginine methyltransferase CARM1/0.442
3af1GDPPantothenate kinase2.7.1.330.442
3b82NADExotoxin A2.4.2.360.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
3zxiTYATyrosine--tRNA ligase, mitochondrial6.1.1.10.442
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.442
4bfvZVVPantothenate kinase2.7.1.330.442
4djv0KMBeta-secretase 13.4.23.460.442
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
4uugPXGBranched-chain amino acid aminotransferase, putative/0.442
5dsyUHBPoly [ADP-ribose] polymerase 22.4.2.300.442
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.441
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.441
3br3ETHTH-type transcriptional regulator QacR/0.441
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3l6jZ90Alr2278 protein/0.441
3p2oNADBifunctional protein FolD/0.441
3zc3FADFerredoxin--NADP reductase1.18.1.20.441
4fam0SZAldo-keto reductase family 1 member C3/0.441
4iae1DXAlr2278 protein/0.441
2rh1CAUBeta-2 adrenergic receptor/0.441
1gveNAPAflatoxin B1 aldehyde reductase member 310.440
1x1bSAHC-20 methyltransferase/0.440
2cekN8TAcetylcholinesterase3.1.1.70.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2jj8AZZDeoxynucleoside kinase/0.440
2vq7NAPPutative flavin-containing monooxygenase/0.440
2wzySQXSoluble acetylcholine receptor/0.440
2xugTZ4Acetylcholinesterase3.1.1.70.440
2xuiTZ5Acetylcholinesterase3.1.1.70.440
2xuoTZ4Acetylcholinesterase3.1.1.70.440
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3znoSE5D-amino-acid oxidase1.4.3.30.440
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.440
4glx0XSDNA ligase6.5.1.20.440
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
4lc71WPBeta-secretase 13.4.23.460.440
5d6lCAUBeta-2 adrenergic receptor/0.440