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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
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.41

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.411.000
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.612
2aqbTL63-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.602
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.596
4c717RD3-oxoacyl-ACP synthase/0.593
4c6zTLE3-oxoacyl-ACP synthase/0.574
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.573
4c72TLG3-oxoacyl-ACP synthase/0.566
3hnzPMN3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.565
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.561
4c73TLH3-oxoacyl-ACP synthase/0.561
4jv3N32Beta-ketoacyl synthase/0.553
3g11P9C3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.547
2gfxPMN3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.538
3ho2N323-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.536
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.518
4c6uTLG3-oxoacyl-ACP synthase/0.516
3fhxPXLPyridoxal kinase2.7.1.350.497
2wggTLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.495
4b1rITCTetracycline repressor protein class D/0.492
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.486
1aiqCB3Thymidylate synthase/0.484
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.479
3ha7B32Hydroxymycolate synthase MmaA42.1.10.478
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.477
1juvNDPDihydrofolate reductase1.5.1.30.475
2uxoTACHTH-type transcriptional regulator TtgR/0.475
4bfvZVVPantothenate kinase2.7.1.330.474
4h3f10OBeta-secretase 13.4.23.460.471
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.470
2w6qOA5Biotin carboxylase6.3.4.140.469
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.469
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
1kqwRTLCellular retinol-binding protein type II/0.468
2ym1FADPhenylacetone monooxygenase1.14.13.920.468
5fkoTDCTetracycline repressor protein class D/0.467
1eioGCHGastrotropin/0.466
1xddAAYIntegrin alpha-L/0.466
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
1thnADPAnti-sigma F factor/0.464
1qorNDPQuinone oxidoreductase 1/0.463
3otwCOAPhosphopantetheine adenylyltransferase/0.463
3qwbNDPProbable quinone oxidoreductase1.6.5.50.463
4bfuZVUPantothenate kinase2.7.1.330.463
3bk2U5PRibonuclease J/0.462
4oztP1AEcdysone receptor, putative/0.462
1ez0NAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.461
2gjlFMNNitronate monooxygenase1.13.12.160.460
2gv8NDPThiol-specific monooxygenase1.14.130.460
3ixp834Ecdysone receptor/0.460
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.460
4qzuRTLRetinol-binding protein 2/0.460
1orkATCTetracycline repressor protein class D/0.459
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.459
3fhxPLPPyridoxal kinase2.7.1.350.459
4bfxZVXPantothenate kinase2.7.1.330.459
4i6gFADCryptochrome-2/0.459
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.458
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.458
3rdqDTBStreptavidin/0.458
4bmpFMNProtein NrdI/0.458
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
5fklTDCTetracycline repressor protein class D/0.458
1a8pFADFerredoxin--NADP reductase/0.457
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.457
2vd0D27Hematopoietic prostaglandin D synthase/0.457
3br3ETHTH-type transcriptional regulator QacR/0.457
3h3qH13Collagen type IV alpha-3-binding protein/0.457
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.457
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.457
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.456
2hk9NAPShikimate dehydrogenase (NADP(+))/0.456
2jb4A14Isopenicillin N synthase1.21.3.10.456
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.456
3v2uATPProtein GAL3/0.456
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.455
1tysDHFThymidylate synthase/0.455
1x8lOXRRetinol dehydratase/0.455
2vceU2FUDP-glycosyltransferase 72B1/0.455
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.455
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.454
1vbiNADMalate/L-lactate dehydrogenase family protein/0.454
1ykdCMPAdenylate cyclase/0.454
2x9dITCTetracycline repressor protein class D/0.454
3arvSAUChitinase A/0.454
3h3sH15Collagen type IV alpha-3-binding protein/0.454
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.454
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.454
5ig2NADShort-chain dehydrogenase/reductase SDR/0.454
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
2i4qUA4Renin3.4.23.150.453
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.453
1f20FADNitric oxide synthase, brain1.14.13.390.452
2fj1CTCTetracycline repressor protein class D/0.452
2xlpNAPPutative flavin-containing monooxygenase/0.452
4auxXTCTetracycline repressor protein class D/0.452
4bftZVTPantothenate kinase2.7.1.330.452
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.452
4m83ERYOleandomycin glycosyltransferase2.4.10.452
4u8iFDAUDP-galactopyranose mutase/0.452
2ed3SAHDiphthine synthase/0.451
2tctCTCTetracycline repressor protein class D/0.451
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
4b3aTACTetracycline repressor protein class D/0.451
4bj9UHBTankyrase-22.4.2.300.451
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
5dp2NAPCurF/0.451
5irnADPNucleotide binding oligomerization domain containing 2/0.451
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.450
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.450
2eldSAHDiphthine synthase/0.450
2vqoTFGHistone deacetylase 43.5.1.980.450
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.450
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.450
4li81XQTankyrase-12.4.2.300.450
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.450
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.450
4zj8SUVOrexin receptor type 1/0.450
1k7fIAVTryptophan synthase alpha chain/0.449
1xzqFONtRNA modification GTPase MnmE3.6.50.449
2cleF6FTryptophan synthase alpha chain/0.449
2ejvNADL-threonine 3-dehydrogenase/0.449
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.449
2qimZEAClass 10 plant pathogenesis-related protein/0.449
2vbdV10Isopenicillin N synthase1.21.3.10.449
2wgeTLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.449
3gncQQQGlutaryl-CoA dehydrogenase/0.449
3ijdC2FMethylenetetrahydrofolate reductase/0.449
4a81DXCMajor pollen allergen Bet v 1-A/0.449
4eb5PLPCysteine desulfurase IscS 2/0.449
2eniSAHDiphthine synthase/0.448
2x6o2TCTetracycline repressor protein class D/0.448
2x7hPFNProstaglandin reductase 310.448
2xpuTDCTetracycline repressor protein class D/0.448
4g090VDHistidinol dehydrogenase/0.448
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
1tduCB3Thymidylate synthase/0.447
2cftPLPPyridoxal phosphate phosphatase/0.447
3mdvCL6Cholesterol 24-hydroxylase/0.447
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.447
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3thyADPDNA mismatch repair protein Msh2/0.447
3zkyWT4Isopenicillin N synthase1.21.3.10.447
4c0bATPmRNA cleavage and polyadenylation factor CLP1/0.447
4rww2BALmo2692 protein/0.447
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.447
5stdUNNScytalone dehydratase4.2.1.940.447
1j9zFADNADPH--cytochrome P450 reductase/0.446
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.446
1v35NAIEnoyl-ACP reductase/0.446
2dv3SAHDiphthine synthase/0.446
2vwu7X1Ephrin type-B receptor 42.7.10.10.446
2zevB71Geranylgeranyl pyrophosphate synthase/0.446
3e2sFADBifunctional protein PutA1.5.5.20.446
4dc0NDPPutative ketoacyl reductase1.3.10.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
5dbfNDPIridoid synthase1.3.1.990.446
1crbRTLRetinol-binding protein 1/0.445
1r2jFADFkbI/0.445
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.445
3gwfFADCyclohexanone monooxygenase/0.445
3iogSDFMetallo-beta-lactamase type 2/0.445
3pm1ETHTH-type transcriptional regulator QacR/0.445
3vmmP0DAlanine--anticapsin ligase/0.445
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
4bfyZVYPantothenate kinase2.7.1.330.445
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.445
4ez8DHFThymidylate synthase2.1.1.450.445
4guuFA9Lysine-specific histone demethylase 1B10.445
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.445
5fm7ADPRuvB-like helicase/0.445
1mczRMNBenzoylformate decarboxylase4.1.1.70.444
1sq5ADPPantothenate kinase2.7.1.330.444
1udaUFGUDP-glucose 4-epimerase5.1.3.20.444
2ekaSAHDiphthine synthase/0.444
3ojxFMNNADPH--cytochrome P450 reductase/0.444
3tifADPUncharacterized ABC transporter ATP-binding protein MJ0796/0.444
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.444
4ipw1G7Mycocyclosin synthase1.14.21.90.444
5fl3ADPPili retraction protein PilT/0.444
5jy1NADPutative short-chain dehydrogenase/reductase/0.444
1dirNADDihydropteridine reductase1.5.1.340.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.443
2nn7M29Carbonic anhydrase 14.2.1.10.443
2q9fC3SCholesterol 24-hydroxylase/0.443
2uxhQUEHTH-type transcriptional regulator TtgR/0.443
3q43D66M1 family aminopeptidase3.4.110.443
3tm5SFGUncharacterized protein/0.443
4g7gVFVLanosterol 14-alpha-demethylase/0.443
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1tllFADNitric oxide synthase, brain1.14.13.390.442
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3m6pBB2Peptide deformylase 1B, chloroplastic/mitochondrial3.5.1.880.442
3rupADPBiotin carboxylase6.3.4.140.442
3toxNAPPutative oxidoreductase/0.442
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4b2gV1NUncharacterized protein/0.442
4iawLIZNeutrophil gelatinase-associated lipocalin/0.442
4tkg09LTankyrase-22.4.2.300.442
1cjkFOKAdenylate cyclase type 2/0.441
1cjkFOKAdenylate cyclase type 5/0.441
1cjvFOKAdenylate cyclase type 2/0.441
1cjvFOKAdenylate cyclase type 5/0.441
1i59ANPChemotaxis protein CheA2.7.13.30.441
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.441
1kt3RTLRetinol-binding protein 4/0.441
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.441
2bu9HFVIsopenicillin N synthase1.21.3.10.441
2g1r3IGRenin3.4.23.150.441
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.441
2vnkFADNADPH:ferredoxin reductase/0.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3vyfVYFRenin3.4.23.150.441
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.441
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
4isg1FYGlucokinase2.7.1.20.441
4l8u9AZSerum albumin/0.441
1bmfANPATP synthase subunit alpha, mitochondrial/0.440
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.440
1ppjANYCytochrome b/0.440
2c3p1TPPyruvate synthase/0.440
2dknNAI3-alpha-hydroxysteroid dehydrogenase/0.440
2e07SAHDiphthine synthase/0.440
2egbSAHDiphthine synthase/0.440
3adaNADSubunit alpha of sarocosine oxidase/0.440
3cndFADPolyamine oxidase FMS1/0.440
3d5qT30Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4b4vL34Bifunctional protein FolD/0.440
4bfsZVSPantothenate kinase2.7.1.330.440
4cdmFO1Deoxyribodipyrimidine photolyase/0.440
4g3jVNTLanosterol 14-alpha-demethylase/0.440
4mihFADPyranose 2-oxidase1.1.3.100.440
4nb6444Nuclear receptor ROR-gamma/0.440
5hs1VORLanosterol 14-alpha demethylase/0.440