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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
5a28MYAGlycylpeptide N-tetradecanoyltransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5a28MYAGlycylpeptide N-tetradecanoyltransferase/1.000
4a2zMYAGlycylpeptide N-tetradecanoyltransferase/0.811
4cgpMYAGlycylpeptide N-tetradecanoyltransferase/0.791
5ag6MYAGlycylpeptide N-tetradecanoyltransferase/0.733
2wsaMYAGlycylpeptide N-tetradecanoyltransferase/0.723
4a30MYAGlycylpeptide N-tetradecanoyltransferase/0.708
5a27MYAGlycylpeptide N-tetradecanoyltransferase/0.704
4ucnMYAGlycylpeptide N-tetradecanoyltransferase/0.703
5ag7MYAGlycylpeptide N-tetradecanoyltransferase/0.697
4a32MYAGlycylpeptide N-tetradecanoyltransferase/0.695
4c68NHWGlycylpeptide N-tetradecanoyltransferase/0.667
2wuuNHWGlycylpeptide N-tetradecanoyltransferase/0.665
4bbhNHWGlycylpeptide N-tetradecanoyltransferase/0.657
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.651
4a33MYAGlycylpeptide N-tetradecanoyltransferase/0.628
4b11NHWGlycylpeptide N-tetradecanoyltransferase/0.623
4c2zMYAGlycylpeptide N-tetradecanoyltransferase 1/0.623
4c2xNHWGlycylpeptide N-tetradecanoyltransferase 2/0.616
2yneNHWGlycylpeptide N-tetradecanoyltransferase/0.614
4b12NHWGlycylpeptide N-tetradecanoyltransferase/0.610
2yncYNCGlycylpeptide N-tetradecanoyltransferase/0.604
4b10NHWGlycylpeptide N-tetradecanoyltransferase/0.600
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.592
4a95NHWGlycylpeptide N-tetradecanoyltransferase/0.586
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.582
4b13NHWGlycylpeptide N-tetradecanoyltransferase/0.578
4b14NHWGlycylpeptide N-tetradecanoyltransferase/0.560
5ag5MYAGlycylpeptide N-tetradecanoyltransferase/0.560
1iidNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.555
2nmtNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.554
4qbjNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.530
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.514
4j6cSTRCytochrome P450 monooxygenase/0.505
4jbtASDCytochrome P450 monooxygenase/0.503
3abaFLICytochrome P450/0.501
5bp9SAHPutative methyltransferase protein/0.499
4j6dTESCytochrome P450 monooxygenase/0.497
4uymVOR14-alpha sterol demethylase Cyp51B/0.497
3tdaPN0Cytochrome P450 2D6/0.495
3s1dZIRCytokinin dehydrogenase 11.5.99.120.492
3p6pA6BCamphor 5-monooxygenase1.14.15.10.491
5jtbZMAAdenosine receptor A2a/0.490
3p6nDSOCamphor 5-monooxygenase1.14.15.10.488
5k2cZMAAdenosine receptor A2a/0.488
5k2bZMAAdenosine receptor A2a/0.488
5k2aZMAAdenosine receptor A2a/0.487
3pwhZMAAdenosine receptor A2a/0.487
2z3uCRRCytochrome P450/0.486
5dp2NAPCurF/0.486
4j6bPLOCytochrome P450 monooxygenase/0.485
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.483
4iaq2GM5-hydroxytryptamine receptor 1B/0.483
4jlj1NMDeoxycytidine kinase2.7.1.740.483
2x23TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.480
2yjxYJXHeat shock protein HSP 90-alpha/0.480
3sfi3SFHTH-type transcriptional regulator EthR/0.479
3l0lHC3Nuclear receptor ROR-gamma/0.478
1re9DSOCamphor 5-monooxygenase1.14.15.10.477
1tysDHFThymidylate synthase/0.477
4iarERM5-hydroxytryptamine receptor 1B/0.477
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.476
1xddAAYIntegrin alpha-L/0.475
3a1l2CCCytochrome P450/0.475
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.475
3v94WYQPhosphodiesterase/0.474
2ykjYKJHeat shock protein HSP 90-alpha/0.473
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.472
3p6oETGCamphor 5-monooxygenase1.14.15.10.471
4nieNBHNuclear receptor ROR-gamma/0.471
3gc8B45Mitogen-activated protein kinase 112.7.11.240.470
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.470
1diuBDMDihydrofolate reductase1.5.1.30.469
3bgrT27Gag-Pol polyprotein2.7.7.490.469
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.469
1cjwCOTSerotonin N-acetyltransferase/0.468
1disBDMDihydrofolate reductase1.5.1.30.468
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.468
5a3cNADSIR2 family protein/0.468
3p6mDSOCamphor 5-monooxygenase1.14.15.10.467
4bqg50QHeat shock protein HSP 90-alpha/0.467
4h4o506Gag-Pol polyprotein2.7.7.490.467
4ifvT27Gag-Pol polyprotein2.7.7.490.467
4at0FADPossible succinate dehydrogenase/0.466
1j3iWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.465
1zhzERGOxysterol-binding protein homolog 4/0.465
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.465
3h1jSMACytochrome b/0.465
3qlhT27Gag-Pol polyprotein2.7.7.490.465
5k2dZMAAdenosine receptor A2a/0.465
2ykbYKBHeat shock protein HSP 90-alpha/0.464
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.464
4g3jVNTLanosterol 14-alpha-demethylase/0.464
1ezfIN0Squalene synthase2.5.1.210.462
1h35R01Squalene--hopene cyclase4.2.1.1290.462
2pnuENMAndrogen receptor/0.462
2ykiYKIHeat shock protein HSP 90-alpha/0.462
3mnrSD1Heat shock protein HSP 90-alpha/0.462
4ib4ERM5-hydroxytryptamine receptor 2B/0.462
1cqp803Integrin alpha-L/0.461
1uyePU9Heat shock protein HSP 90-alpha/0.461
3qm4PN0Cytochrome P450 2D6/0.461
3qwbNDPProbable quinone oxidoreductase1.6.5.50.461
3fowIMHPurine nucleoside phosphorylase/0.460
3hu3AGSTransitional endoplasmic reticulum ATPase3.6.4.60.460
3i0pNADMalate dehydrogenase, putative/0.460
3q43D66M1 family aminopeptidase3.4.110.460
4o7uTHFThymidylate synthase/0.460
1mc5AHEAlcohol dehydrogenase class-31.1.1.10.459
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.459
4iah1DXAlr2278 protein/0.459
4o95245Cytokinin dehydrogenase 4/0.459
5uviZMAAdenosine receptor A2a/0.459
2bifANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 42.7.1.1050.458
2ykcYKCHeat shock protein HSP 90-alpha/0.458
2ylwFADPhenylacetone monooxygenase1.14.13.920.458
2zd1T27Gag-Pol polyprotein2.7.7.490.458
3bqdDAYGlucocorticoid receptor/0.458
3uwlFOZThymidylate synthase/0.458
4l9q9TPSerum albumin/0.458
3rfmCFFAdenosine receptor A2a/0.458
1o6rR19Squalene--hopene cyclase4.2.1.1290.457
2braFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.457
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.457
2yk2YJXHeat shock protein HSP 90-alpha/0.457
3dl9V2HVitamin D 25-hydroxylase/0.457
3jynNDPQuinone oxidoreductase/0.457
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.457
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.457
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.457
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.457
1upw444Oxysterols receptor LXR-beta/0.456
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.456
3kpkFADSulfide-quinone reductase/0.456
4eevL1XHepatocyte growth factor receptor2.7.10.10.456
4ktf1TMCytochrome P450/0.456
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.455
3ua108YCytochrome P450 3A4/0.455
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.455
4do30LAFatty-acid amide hydrolase 13.5.1.990.455
4i8vBHFCytochrome P450 1A11.14.14.10.455
4jlk1NODeoxycytidine kinase2.7.1.740.455
4mfpCOAUncharacterized protein/0.455
4nxwADPMitochondrial dynamics protein MID51/0.455
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
1tduCB3Thymidylate synthase/0.454
4b4w9L9Bifunctional protein FolD/0.454
4rv9SAHD-mycarose 3-C-methyltransferase/0.454
1jg0DDTThymidylate synthase/0.453
1pqc444Oxysterols receptor LXR-beta/0.453
1qorNDPQuinone oxidoreductase 1/0.453
1sqi8694-hydroxyphenylpyruvate dioxygenase/0.453
1tl7ONMAdenylate cyclase type 2/0.453
1tl7ONMAdenylate cyclase type 5/0.453
1zhwHC2Oxysterol-binding protein homolog 4/0.453
2gd0MRSProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.453
2zb8IMNProstaglandin reductase 21.3.1.480.453
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
4eiyZMAAdenosine receptor A2a/0.453
1o6qR17Squalene--hopene cyclase4.2.1.1290.452
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.452
3e5aVX6Aurora kinase A2.7.11.10.452
3q0vLL4HTH-type transcriptional regulator EthR/0.452
4ez8DHFThymidylate synthase2.1.1.450.452
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.452
4isk1JYThymidylate synthase/0.452
4ko8AGSTransitional endoplasmic reticulum ATPase3.6.4.60.452
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
3uzcT4EAdenosine receptor A2a/0.452
1ie8KH1Vitamin D3 receptor/0.451
2w4qCBWProstaglandin reductase 21.3.1.480.451
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.451
3o8gO8GHTH-type transcriptional regulator EthR/0.451
4id5T27Gag-Pol polyprotein2.7.7.490.451
3uzaT4GAdenosine receptor A2a/0.451
1dajMOTDihydrofolate reductase1.5.1.30.450
1ie9VDXVitamin D3 receptor/0.450
1ppjSMACytochrome b/0.450
1sqvUHDCytochrome b/0.450
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2fmn4HF5,10-methylenetetrahydrofolate reductase1.5.1.200.450
2z2w770Wee1-like protein kinase2.7.10.20.450
3cseN22Uncharacterized protein/0.450
3ol5SAWCamphor 5-monooxygenase1.14.15.10.450
4nh82LCHeat shock protein HSP 90-alpha/0.450
1h36R88Squalene--hopene cyclase4.2.1.1290.449
3s79ASDAromatase1.14.14.140.449
3tm5SFGUncharacterized protein/0.449
4h8004TAldehyde dehydrogenase, dimeric NADP-preferring/0.449
1ep4S11Gag-Pol polyprotein2.7.7.490.448
1pkfEPDEpothilone C/D epoxidase1.140.448
1s19MC9Vitamin D3 receptor/0.448
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.448
3cid318Beta-secretase 13.4.23.460.448
3up3XCAaceDAF-12/0.448
3vt9YI4Vitamin D3 receptor/0.448
4nxvGDPMitochondrial dynamics protein MID51/0.448
5ab6CAANonspecific lipid-transfer protein, putative/0.448
7dfrFOLDihydrofolate reductase1.5.1.30.448
5iu86DZAdenosine receptor A2a/0.448
1ci7CB3Thymidylate synthase2.1.1.450.447
1fwmCB3Thymidylate synthase/0.447
1kceCB3Thymidylate synthase/0.447
1krrACOGalactoside O-acetyltransferase2.3.1.180.447
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.447
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.447
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.447
2b378PSEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3cxhSMACytochrome b/0.447
3hz137DHeat shock protein HSP 90-alpha/0.447
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3p99LNPLanosterol 14-alpha-demethylase/0.447
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4da0GNGPurine nucleoside phosphorylase DeoD-type2.4.2.10.447
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4k4eK4ETankyrase-12.4.2.300.447
1uydPU8Heat shock protein HSP 90-alpha/0.446
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.446
3nx4NAPPutative oxidoreductase/0.446
4b4vL34Bifunctional protein FolD/0.446
1oc1ASVIsopenicillin N synthase1.21.3.10.445
1uyfPU1Heat shock protein HSP 90-alpha/0.445
2ovhAS0Progesterone receptor/0.445
3cp9C19Vascular endothelial growth factor receptor 22.7.10.10.445
3gwfFADCyclohexanone monooxygenase/0.445
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.445
3invC50Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.445
4jqh1MFAlr2278 protein/0.445
4pd6URINucleoside permease/0.445
7catNDPCatalase1.11.1.60.445
1cc2FADCholesterol oxidase1.1.3.60.444
1kzjCB3Thymidylate synthase/0.444
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2i9pNAD3-hydroxyisobutyrate dehydrogenase, mitochondrial1.1.1.310.444
2q9fC3SCholesterol 24-hydroxylase/0.444
2ykeYKEHeat shock protein HSP 90-alpha/0.444
3up4NAP2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
3vt8YI3Vitamin D3 receptor/0.444
3wmxNADNAD dependent epimerase/dehydratase/0.444
4echFADPolyamine oxidase FMS1/0.444
4elf35IDihydrofolate reductase/0.444
4h3i10VBeta-secretase 13.4.23.460.444
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.444
4x7ySAHMycinamicin III 3''-O-methyltransferase2.1.1.2370.444
5dozNDPJamJ/0.444
1ppjANYCytochrome b/0.443
1uymPU3Heat shock protein HSP 90-beta/0.443
2zevB71Geranylgeranyl pyrophosphate synthase/0.443
3g70A5TRenin3.4.23.150.443
3ghwGHWDihydrofolate reductase1.5.1.30.443
3mg3ECHOrange carotenoid-binding protein/0.443
3nfaCBJGag-Pol polyprotein/0.443
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4foxD16Thymidylate synthase ThyA/0.443
4l06NAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.443
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.443
4rw6494Gag-Pol polyprotein2.7.7.490.443
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.443
1cd2FOLDihydrofolate reductase1.5.1.30.442
1kk4ACOStreptogramin A acetyltransferase2.3.10.442
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2fzhDH1Dihydrofolate reductase1.5.1.30.442
2hasC3OVitamin D3 receptor/0.442
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.442
3freTOPDihydrofolate reductase1.5.1.30.442
3hu2AGSTransitional endoplasmic reticulum ATPase3.6.4.60.442
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.442
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.442
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
4i2pG73Gag-Pol polyprotein2.7.7.490.442
4ia1BIVVitamin D3 receptor A/0.442
4nb6444Nuclear receptor ROR-gamma/0.442
4phlPILPhosphodiesterase/0.442
4ylhYE1(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase/0.442
1f4fTP3Thymidylate synthase/0.441
1o5rFR9Adenosine deaminase3.5.4.40.441
1p44GEQEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1trgCB3Thymidylate synthase/0.441
1uy9PU6Heat shock protein HSP 90-alpha/0.441
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2hb7O1CVitamin D3 receptor/0.441
2panTDPGlyoxylate carboligase4.1.1.470.441
4dhyS41Glucokinase2.7.1.20.441
4gqkADPActin cross-linking toxin VgrG1/0.441
4ug71EVNitric oxide synthase oxygenase1.14.13.1650.441
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.441
4ug2NGIAdenosine receptor A2a/0.441
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.440
1jlaTNKGag-Pol polyprotein2.7.7.490.440
1khrCOAStreptogramin A acetyltransferase2.3.10.440
1rdtL79Retinoic acid receptor RXR-alpha/0.440
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.440
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.440
2in6839Wee1-like protein kinase2.7.10.20.440
2qjpSMACytochrome b/0.440
2qu6857Vascular endothelial growth factor receptor 22.7.10.10.440
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3slkNDPPolyketide synthase extender module 2/0.440
3vt5YI2Vitamin D3 receptor/0.440
4elg52JDihydrofolate reductase/0.440
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4i9i1DYTankyrase-12.4.2.300.440
4itfTFYVitamin D3 receptor/0.440
4jpc1M6Beta-secretase 13.4.23.460.440
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.440
3qakUKAAdenosine receptor A2a/0.440