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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
3dz4C8MS-adenosylmethionine decarboxylase proenzyme4.1.1.50

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3dz4C8MS-adenosylmethionine decarboxylase proenzyme4.1.1.501.000
3dz2A8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.787
3dz6M8ES-adenosylmethionine decarboxylase proenzyme4.1.1.500.743
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.686
3h0wN8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.678
3h0vM2TS-adenosylmethionine decarboxylase proenzyme4.1.1.500.597
1i7mCGS-adenosylmethionine decarboxylase proenzyme4.1.1.500.568
1i7cMGBS-adenosylmethionine decarboxylase proenzyme4.1.1.500.559
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.526
1u65CP0Acetylcholinesterase3.1.1.70.513
2w6cBM4Acetylcholinesterase3.1.1.70.511
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.498
2ejzSAHDiphthine synthase/0.494
2j83BATUlilysin3.4.240.494
2v57PRLTetR family transcriptional regulator/0.493
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.493
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.489
4a86H35Major pollen allergen Bet v 1-A/0.488
3qgf46FGenome polyprotein2.7.7.480.487
4arbC57Acetylcholinesterase3.1.1.70.487
3hl0NADMaleylacetate reductase/0.486
4hmwFMNPyridoxamine 5'-phosphate oxidase/0.486
1q84TZ4Acetylcholinesterase3.1.1.70.485
1eveE20Acetylcholinesterase3.1.1.70.484
4a81DXCMajor pollen allergen Bet v 1-A/0.484
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.483
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
1xf0ASDAldo-keto reductase family 1 member C3/0.477
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.477
2xuqTZ4Acetylcholinesterase3.1.1.70.474
4araC56Acetylcholinesterase3.1.1.70.474
1odjGMPPurine nucleoside phosphorylase/0.473
2j3qTFLAcetylcholinesterase3.1.1.70.473
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.473
1jdzFMBPurine nucleoside phosphorylase/0.472
1ry8RUTAldo-keto reductase family 1 member C3/0.472
1wkhPPE[LysW]-aminoadipate semialdehyde transaminase/0.472
1w4lGL8Acetylcholinesterase3.1.1.70.471
2xukTZ5Acetylcholinesterase3.1.1.70.471
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.470
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.470
4frkDWDBeta-secretase 13.4.23.460.470
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.469
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.469
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.468
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.468
4uymVOR14-alpha sterol demethylase Cyp51B/0.468
1h22E10Acetylcholinesterase3.1.1.70.467
1ry0PG2Aldo-keto reductase family 1 member C3/0.467
2xlpNAPPutative flavin-containing monooxygenase/0.467
2zs9ADPPantothenate kinase2.7.1.330.467
4bprFADFerredoxin--NADP reductase1.18.1.20.467
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.466
3qe2FMNNADPH--cytochrome P450 reductase/0.465
2gyuHI6Acetylcholinesterase3.1.1.70.464
2xytTC9Soluble acetylcholine receptor/0.464
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.464
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.463
5a4vQUEGlutathione S-transferase F22.5.1.180.463
1amoFMNNADPH--cytochrome P450 reductase/0.462
3af1GDPPantothenate kinase2.7.1.330.462
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.461
3p0fBAUUridine phosphorylase 22.4.2.30.461
3zkyWT4Isopenicillin N synthase1.21.3.10.461
4dbs0HVAldo-keto reductase family 1 member C3/0.461
4plpNADHomospermidine synthase2.5.1.440.461
1psa0ZLPepsin A3.4.23.10.460
1zgbA1EAcetylcholinesterase3.1.1.70.460
2xupTZ5Acetylcholinesterase3.1.1.70.460
2zevIPEGeranylgeranyl pyrophosphate synthase/0.460
3vf60H6Glucokinase2.7.1.20.460
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.460
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.460
4jtqFLPAldo-keto reductase family 1 member C2/0.460
4nv1TYDFormyl transferase/0.460
4psbGA3Cytokinin-specific binding protein/0.460
1odcA8BAcetylcholinesterase3.1.1.70.459
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.459
2g1y5IGRenin3.4.23.150.459
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.459
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.459
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.459
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.459
4j7gTRHPCZA361.3/0.459
4m0f1YKAcetylcholinesterase3.1.1.70.459
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.458
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.458
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.458
1zzuDP1Nitric oxide synthase, brain1.14.13.390.458
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.458
4e32DWNMethyltransferase/0.458
1wkgPOI[LysW]-aminoadipate semialdehyde transaminase/0.456
2xysSY9Soluble acetylcholine receptor/0.456
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.456
1lc3NADBiliverdin reductase A1.3.1.240.455
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.455
2xufTZ4Acetylcholinesterase3.1.1.70.455
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.455
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
4b7zQ4QAcetylcholinesterase3.1.1.70.455
4bb3KKAIsopenicillin N synthase1.21.3.10.455
4ey7E20Acetylcholinesterase3.1.1.70.455
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.455
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.455
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.454
1g63FMNEpidermin decarboxylase4.1.10.454
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.454
2g8yNADHydroxycarboxylate dehydrogenase B/0.454
2gpjFADSiderophore-interacting protein/0.454
2gywOBIAcetylcholinesterase3.1.1.70.454
2qimZEAClass 10 plant pathogenesis-related protein/0.454
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1hb3SCVIsopenicillin N synthase1.21.3.10.453
1pqc444Oxysterols receptor LXR-beta/0.453
1qtiGNTAcetylcholinesterase3.1.1.70.453
1ut6A8NAcetylcholinesterase3.1.1.70.453
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.453
3ndjJHZMethyltransferase/0.453
3uayADNPurine nucleoside phosphorylase DeoD-type/0.453
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.453
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.453
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.453
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.452
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.452
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.452
4xrgNADHomospermidine synthase2.5.1.440.452
1sm4FADFerredoxin--NADP reductase/0.451
3l6jZ90Alr2278 protein/0.451
1fmlRTLRetinol dehydratase/0.450
1icqOPD12-oxophytodienoate reductase 11.3.1.420.450
1xh5R68cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.450
2uxoTACHTH-type transcriptional regulator TtgR/0.450
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.450
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1bk0ACVIsopenicillin N synthase1.21.3.10.449
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
2cnsACORibosomal-protein-alanine acetyltransferase/0.449
2fxuBIDActin, alpha skeletal muscle/0.449
2j9lATPH(+)/Cl(-) exchange transporter 5/0.449
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.449
3s5wFADL-ornithine N(5)-monooxygenase/0.449
4e2yJHZMethyltransferase/0.449
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.449
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.449
4usrFADMonooxygenase/0.449
5ds309LPoly [ADP-ribose] polymerase 12.4.2.300.449
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.448
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3rsv3RSBeta-secretase 13.4.23.460.448
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.448
4p9dTMPDeoxycytidylate deaminase/0.448
4xwtU5PRibonuclease J/0.448
1blzACVIsopenicillin N synthase1.21.3.10.447
1q83TZ5Acetylcholinesterase3.1.1.70.447
1s1rNAPAldo-keto reductase family 1 member C3/0.447
2gesCOKPantothenate kinase2.7.1.330.447
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.447
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.447
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3g72A6TRenin3.4.23.150.447
4relKMPGlycosyltransferase/0.447
2yczI32Beta-1 adrenergic receptor/0.447
1p8dCO1Oxysterols receptor LXR-beta/0.446
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.446
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
1xvaSAMGlycine N-methyltransferase2.1.1.200.446
2bn4FMNNADPH--cytochrome P450 reductase/0.446
2ckmAA7Acetylcholinesterase3.1.1.70.446
2jl1NAPTriphenylmethane reductase/0.446
3br3ETHTH-type transcriptional regulator QacR/0.446
3ensENSCoagulation factor X3.4.21.60.446
3ko8NADNAD-dependent epimerase/dehydratase/0.446
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.446
4g090VDHistidinol dehydrogenase/0.446
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.445
1lnmDTXBilin-binding protein/0.445
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2abaSTRPentaerythritol tetranitrate reductase/0.445
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.445
3vg10GTBeta-secretase 13.4.23.460.445
3vjcZGASqualene synthase2.5.1.210.445
4l65C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.445
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
4xvySAHMycinamicin III 3''-O-methyltransferase2.1.1.2370.445
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.444
2ha6SCKAcetylcholinesterase3.1.1.70.444
2vq7NAPPutative flavin-containing monooxygenase/0.444
2wnbC5PCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 12.4.99.40.444
2ylxNAPPhenylacetone monooxygenase1.14.13.920.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3pn1IVHDNA ligase/0.444
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.443
2weaPP6Penicillopepsin-13.4.23.200.443
2xujTZ5Acetylcholinesterase3.1.1.70.443
2y0jAXCcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2y1w849Histone-arginine methyltransferase CARM1/0.443
2y1x845Histone-arginine methyltransferase CARM1/0.443
2zsaADPPantothenate kinase2.7.1.330.443
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3rkuNAPNADP-dependent 3-hydroxy acid dehydrogenase/0.443
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.443
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.443
4b65NDPL-ornithine N(5)-monooxygenase/0.443
4epq0RRPoly(ADP-ribose) glycohydrolase/0.443
4hb9FADUncharacterized protein/0.443
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.443
1vbiNADMalate/L-lactate dehydrogenase family protein/0.442
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2b99RDLRiboflavin synthase2.5.1.90.442
3b82NADExotoxin A2.4.2.360.442
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3in6FMNUncharacterized protein/0.442
3k4nFADPyranose 2-oxidase/0.442
3k8q22APurine nucleoside phosphorylase2.4.2.10.442
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.442
3oafOAGDihydrofolate reductase1.5.1.30.442
3wi2P98cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.442
4kbyC2EStimulator of interferon genes protein/0.442
1pq944BOxysterols receptor LXR-beta/0.441
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2cekN8TAcetylcholinesterase3.1.1.70.441
2wzySQXSoluble acetylcholine receptor/0.441
3ai0PNWBeta-glucosidase/0.441
3cb2GDPTubulin gamma-1 chain/0.441
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.441
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.441
3zc3FADFerredoxin--NADP reductase1.18.1.20.441
3zkpERBErythromycin C-12 hydroxylase1.14.13.1540.441
4a83DXCMajor pollen allergen Bet v 1-A/0.441
4b64NAPL-ornithine N(5)-monooxygenase/0.441
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.441
4q71FADBifunctional protein PutA/0.441
5d4vYGPUncharacterized protein MJ0489/0.441
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.440
2isc223Purine nucleoside phosphorylase, putative/0.440
2xugTZ4Acetylcholinesterase3.1.1.70.440
2xuiTZ5Acetylcholinesterase3.1.1.70.440
2xuoTZ4Acetylcholinesterase3.1.1.70.440
2y035FWBeta-1 adrenergic receptor/0.440
3eufBAUUridine phosphorylase 1/0.440
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3hggCHDCmeR/0.440
3qeoLLTDeoxycytidine kinase2.7.1.740.440
4a87NARMajor pollen allergen Bet v 1-A/0.440
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4djv0KMBeta-secretase 13.4.23.460.440
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.440
4ia05BBcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.440
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.440
4oex5EOcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
5dp2NAPCurF/0.440