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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
4ja81K9Isocitrate dehydrogenase [NADP], mitochondrial1.1.1.42

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ja81K9Isocitrate dehydrogenase [NADP], mitochondrial1.1.1.421.000
3vev0H4Glucokinase2.7.1.20.511
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.493
4i2q1BTGag-Pol polyprotein2.7.7.490.492
4m10ICDProstaglandin G/H synthase 21.14.99.10.489
4dhyS41Glucokinase2.7.1.20.484
2npaMMBPeroxisome proliferator-activated receptor alpha/0.483
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.481
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.481
4im01FVSerine/threonine-protein kinase TBK12.7.11.10.479
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.478
4ia7BIVVitamin D3 receptor A/0.477
2znq401Peroxisome proliferator-activated receptor delta/0.476
3zh8C58Protein kinase C iota type2.7.11.130.476
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.474
4n9iPCGCatabolite expression activator/0.474
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.473
1ke6LS2Cyclin-dependent kinase 22.7.11.220.473
4xldBRLPeroxisome proliferator-activated receptor gamma/0.473
2ath3EAPeroxisome proliferator-activated receptor gamma/0.472
3u4uLNHCasein kinase II subunit alpha2.7.11.10.472
1uomPTIEstrogen receptor/0.471
4a99FADTetX family tetracycline inactivation enzyme/0.471
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.470
3ik6HCZGlutamate receptor 2/0.470
1v0pPVBCell division control protein 2 homolog2.7.11.220.469
2p4yC03Peroxisome proliferator-activated receptor gamma/0.469
2znnS44Peroxisome proliferator-activated receptor alpha/0.469
3rmf20ZCyclin-dependent kinase 22.7.11.220.469
4aknS5BBromodomain-containing protein 2/0.469
4gub0Y4Casein kinase II subunit alpha2.7.11.10.469
3a6qFMNFMN-binding protein/0.468
3a6rFMNFMN-binding protein/0.468
3nga3NGCasein kinase II subunit alpha2.7.11.10.468
3vspEK8Peroxisome proliferator-activated receptor gamma/0.468
1juvNDPDihydrofolate reductase1.5.1.30.467
3mtfA3FActivin receptor type-12.7.11.300.467
4i22IREEpidermal growth factor receptor2.7.10.10.467
1ndeMONEstrogen receptor beta/0.466
2j14GNIPeroxisome proliferator-activated receptor delta/0.466
3t2zFADSulfide-quinone reductase/0.466
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.466
1bygSTUTyrosine-protein kinase CSK/0.465
1fvt106Cyclin-dependent kinase 22.7.11.220.465
2cig1DGDihydrofolate reductase1.5.1.30.465
2vzmNRBCytochrome P450 monooxygenase PikC/0.465
2znpK55Peroxisome proliferator-activated receptor delta/0.465
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.465
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.464
4ia2BIVVitamin D3 receptor A/0.464
4okt198Androgen receptor/0.464
2q8sL92Peroxisome proliferator-activated receptor gamma/0.463
3at4CCKCasein kinase II subunit alpha2.7.11.10.463
4idv13VMitogen-activated protein kinase kinase kinase 142.7.11.250.463
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.463
1txiTX5Vitamin D3 receptor/0.462
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.462
2ovmAS0Progesterone receptor/0.462
2rqfJH3Hemolymph juvenile hormone binding protein/0.462
3gu83GUDeath-associated protein kinase 12.7.11.10.462
4a84DXCMajor pollen allergen Bet v 1-A/0.462
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.462
4kwhNAPReductase homolog/0.462
5cshATPCasein kinase II subunit alpha2.7.11.10.462
2b52D42Cyclin-dependent kinase 22.7.11.220.461
2gtk208Peroxisome proliferator-activated receptor gamma/0.461
3wmxNADNAD dependent epimerase/dehydratase/0.461
1fm9570Peroxisome proliferator-activated receptor gamma/0.460
1om1IQACasein kinase II subunit alpha2.7.11.10.460
1x2hLPALipoate-protein ligase A6.3.1.200.460
3bptQUE3-hydroxyisobutyryl-CoA hydrolase, mitochondrial3.1.2.40.460
3v9v21LPeroxisome proliferator-activated receptor gamma/0.460
2q61SF1Peroxisome proliferator-activated receptor gamma/0.459
3a0iAJIGlucokinase2.7.1.20.459
3rak03ZCyclin-dependent kinase 22.7.11.220.459
3sp9IL2Peroxisome proliferator-activated receptor delta/0.459
1db1VDXVitamin D3 receptor/0.458
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.458
2om9AJAPeroxisome proliferator-activated receptor gamma/0.458
2w06FRVCyclin-dependent kinase 22.7.11.220.458
2zoq5IDMitogen-activated protein kinase 32.7.11.240.458
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.458
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
3dd125DGlycogen phosphorylase, liver form2.4.1.10.458
3vt5YI2Vitamin D3 receptor/0.458
4acm7YGCyclin-dependent kinase 22.7.11.220.458
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
1eh4IC1Casein kinase I homolog 12.7.11.10.457
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
2pobGW4Peroxisome proliferator-activated receptor gamma/0.457
3ofm4B0Casein kinase II subunit alpha'2.7.11.10.457
4a9iP9IBromodomain-containing protein 2/0.457
4bibIEOMitogen-activated protein kinase kinase kinase 52.7.11.250.457
4jlj1NMDeoxycytidine kinase2.7.1.740.457
1p44NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
2gdo12CSerine/threonine-protein kinase Chk12.7.11.10.456
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.456
2wi72KLHeat shock protein HSP 90-alpha/0.456
3s1h56ZCyclin-dependent kinase 22.7.11.220.456
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.456
3w1f1O5Dual specificity protein kinase TTK2.7.12.10.456
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.456
5uviZMAAdenosine receptor A2a/0.456
1k74544Peroxisome proliferator-activated receptor gamma/0.455
1knuYPAPeroxisome proliferator-activated receptor gamma/0.455
1nyxDRFPeroxisome proliferator-activated receptor gamma/0.455
1xddAAYIntegrin alpha-L/0.455
3crzFADFerredoxin--NADP+ reductase/0.455
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.455
3m8qDJZGag-Pol polyprotein2.7.7.490.455
3nwq2NCGag-Pol polyprotein3.4.23.160.455
3rm618ZCyclin-dependent kinase 22.7.11.220.455
3sf6FDAGlutaryl-CoA dehydrogenase/0.455
1ia3TQ5Dihydrofolate reductase1.5.1.30.454
2izt23DCasein kinase I isoform gamma-32.7.11.10.454
2j0k4STFocal adhesion kinase 12.7.10.20.454
2ovhAS0Progesterone receptor/0.454
2znoS44Peroxisome proliferator-activated receptor gamma/0.454
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.454
3r7iX9ICyclin-dependent kinase 22.7.11.220.454
3ral04ZCyclin-dependent kinase 22.7.11.220.454
3umw596Serine/threonine-protein kinase pim-12.7.11.10.454
4cqlNADEstradiol 17-beta-dehydrogenase 81.1.1.620.454
5k2aZMAAdenosine receptor A2a/0.454
1eioGCHGastrotropin/0.453
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.453
1rbqKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.453
1y56FMNUncharacterized protein/0.453
1y56FMN382aa long hypothetical sarcosine oxidase/0.453
2w9hTOPDihydrofolate reductase1.5.1.30.453
3vy5FMNFMN-binding protein/0.453
4a83DXCMajor pollen allergen Bet v 1-A/0.453
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.453
5iu4ZMAAdenosine receptor A2a/0.453
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
2izrBRKCasein kinase I isoform gamma-32.7.11.10.452
2vn0TDZCytochrome P450 2C8/0.452
3gw9VNILanosterol 14-alpha-demethylase/0.452
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.452
4ww0ADPATP-dependent zinc metalloprotease FtsH/0.452
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.451
1rk3VDXVitamin D3 receptor/0.451
1sh9RITGag-Pol polyprotein3.4.23.160.451
3nxe2NCProtease/0.451
3rk708ZCyclin-dependent kinase 22.7.11.220.451
4a81DXCMajor pollen allergen Bet v 1-A/0.451
4hgt15GCasein kinase I isoform delta2.7.11.10.451
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.450
2xnbY8LCyclin-dependent kinase 22.7.11.220.450
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.450
3syiFADSulfide-quinone reductase/0.450
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.450
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.450
4nc3ERM5-hydroxytryptamine receptor 2B/0.450
1ygkRRCPyridoxal kinase2.7.1.350.449
1znqNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.449
2hw2RFPRifampin ADP-ribosyl transferase/0.449
2pogWSTEstrogen receptor/0.449
2pvlP55Casein kinase II subunit alpha2.7.11.10.449
2r3tG4GGag-Pol polyprotein3.4.23.160.449
3cylVITBasic phospholipase A2 homolog piratoxin-2/0.449
3el9DR7Gag-Pol polyprotein3.4.23.160.449
3r8pZ46Cyclin-dependent kinase 22.7.11.220.449
3vs0VS0Tyrosine-protein kinase HCK2.7.10.20.449
3zuyTCHTransporter/0.449
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4g170VNCasein kinase I isoform gamma-32.7.11.10.449
4ia3BIVVitamin D3 receptor A/0.449
1zgyBRLPeroxisome proliferator-activated receptor gamma/0.448
2q59240Peroxisome proliferator-activated receptor gamma/0.448
2yekEAMBromodomain-containing protein 2/0.448
3cehAVEGlycogen phosphorylase, liver form2.4.1.10.448
3d5fL41Peroxisome proliferator-activated receptor delta/0.448
3vbq0F5Serine/threonine-protein kinase pim-12.7.11.10.448
3zdu38RCyclin-dependent kinase-like 32.7.11.220.448
4a9nA9NBromodomain-containing protein 2/0.448
4bjx73BBromodomain-containing protein 4/0.448
1hdrNADDihydropteridine reductase1.5.1.340.447
1xjdSTUProtein kinase C theta type2.7.11.130.447
2izsBRQCasein kinase I isoform gamma-32.7.11.10.447
3be9P04Casein kinase II subunit alpha2.7.11.10.447
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.447
3gcoVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.447
3h0aD30Peroxisome proliferator-activated receptor gamma/0.447
3mqe416Prostaglandin G/H synthase 21.14.99.10.447
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4kioG5KTyrosine-protein kinase ITK/TSK2.7.10.20.447
1s4dSAHUroporphyrinogen-III C-methyltransferase2.1.1.1070.446
2hk9NAPShikimate dehydrogenase (NADP(+))/0.446
2jf9OHTEstrogen receptor/0.446
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.446
2ym1FADPhenylacetone monooxygenase1.14.13.920.446
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.446
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.446
4bidIE8Mitogen-activated protein kinase kinase kinase 52.7.11.250.446
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.446
4jqeANPCasein kinase II subunit alpha2.7.11.10.446
4k181OBSerine/threonine-protein kinase pim-12.7.11.10.446
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.446
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.446
4q73FADBifunctional protein PutA/0.446
4wa9AXITyrosine-protein kinase ABL12.7.10.20.446
1kkq471Peroxisome proliferator-activated receptor alpha/0.445
1xqcAEJEstrogen receptor/0.445
2ic3HBYGag-Pol polyprotein2.7.7.490.445
2uxpCLMHTH-type transcriptional regulator TtgR/0.445
3bgrT27Gag-Pol polyprotein2.7.7.490.445
3bheBZNGag-Pol polyprotein3.4.23.160.445
3cyxROCGag-Pol polyprotein3.4.23.160.445
3grySAMProbable ribosomal RNA small subunit methyltransferase A/0.445
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.445
4g1wG1WMitogen-activated protein kinase 82.7.11.240.445
4mt92D6Tankyrase-12.4.2.300.445
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
1xl2189Gag-Pol polyprotein3.4.23.160.444
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2zbaZBATrichothecene 3-O-acetyltransferase/0.444
3a4vNADNDP-sugar epimerase/0.444
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3b6zCO7Enoyl reductase LovC10.444
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.444
3kgaLX9MAP kinase-activated protein kinase 22.7.11.10.444
3kmwATPIntegrin-linked protein kinase2.7.11.10.444
3p6oETGCamphor 5-monooxygenase1.14.15.10.444
4apuA2KProgesterone receptor/0.444
4c57FEFCyclin-G-associated kinase2.7.11.10.444
4fod0UVALK tyrosine kinase receptor2.7.10.10.444
4hee14RPeroxisome proliferator-activated receptor gamma/0.444
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.444
4j5j478Gag-Pol polyprotein3.4.23.160.444
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.444
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.444
4q0a4OAVitamin D3 receptor A/0.444
4uyf73BBromodomain-containing protein 2/0.444
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.444
5jtbZMAAdenosine receptor A2a/0.444
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
1hiiC20Gag-Pol polyprotein/0.443
1ie8KH1Vitamin D3 receptor/0.443
1s0zEB1Vitamin D3 receptor/0.443
1unlRRCCyclin-dependent-like kinase 52.7.11.10.443
1wsvTHHAminomethyltransferase, mitochondrial/0.443
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.443
2fxdDR7Pol polyprotein/0.443
2hamC33Vitamin D3 receptor/0.443
2hcdBIVVitamin D3 receptor A/0.443
2ibzSMACytochrome b/0.443
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.443
2o12FMNChorismate synthase/0.443
2zdt46CMitogen-activated protein kinase 102.7.11.240.443
3imxB84Glucokinase2.7.1.20.443
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3qlrNDPDihydrofolate reductase1.5.1.30.443
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.443
4ez50RSCyclin-dependent kinase 62.7.11.220.443
4ia1BIVVitamin D3 receptor A/0.443
4j0r1H2Bromodomain-containing protein 4/0.443
5e8ySTUTGF-beta receptor type-22.7.11.300.443
1errRALEstrogen receptor/0.442
1rw8580TGF-beta receptor type-12.7.11.300.442
2po7CHDFerrochelatase, mitochondrial4.99.1.10.442
3k9vCPS1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial/0.442
3mnrSD1Heat shock protein HSP 90-alpha/0.442
3oom507Activin receptor type-12.7.11.300.442
3q5kD1UHeat shock protein 83-1/0.442
3qn8NI7Gag-Pol polyprotein3.4.23.160.442
3qtzX42Cyclin-dependent kinase 22.7.11.220.442
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.442
3v9y24LPeroxisome proliferator-activated receptor gamma/0.442
3vthAP2Carbamoyltransferase/0.442
3w5p4OAVitamin D3 receptor/0.442
4ib4ERM5-hydroxytryptamine receptor 2B/0.442
4oztP1AEcdysone receptor, putative/0.442
5dt4ATPAurora kinase A2.7.11.10.442
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
1k7l544Peroxisome proliferator-activated receptor alpha/0.441
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
1t2bCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.441
1t2cNAIL-lactate dehydrogenase1.1.1.270.441
1y0s331Peroxisome proliferator-activated receptor delta/0.441
2cciATPCyclin-dependent kinase 22.7.11.220.441
2g0gSP0Peroxisome proliferator-activated receptor gamma/0.441
2p3a3TLPol protein/0.441
2r5q1UNGag-Pol polyprotein/0.441
3c6tM14Gag-Pol polyprotein2.7.7.490.441
3ggfGVDSerine/threonine-protein kinase 26/0.441
3h0a9RARetinoic acid receptor RXR-alpha/0.441
3ibqATPPyridoxal kinase/0.441
3kfs3TLGag-Pol polyprotein/0.441
3ufnROCGag-Pol polyprotein/0.441
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.441
4fob0USALK tyrosine kinase receptor2.7.10.10.441
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4irnFADAnaB/0.441
4k0y1OASerine/threonine-protein kinase pim-12.7.11.10.441
4ure1PSCyclohexanol dehydrogenase/0.441
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.441
5dr6SKEAurora kinase A2.7.11.10.441
1ai9NDPDihydrofolate reductase1.5.1.30.440
1s19MC9Vitamin D3 receptor/0.440
1yhsSTUSerine/threonine-protein kinase pim-12.7.11.10.440
2cchATPCyclin-dependent kinase 22.7.11.220.440
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.440
2pnuENMAndrogen receptor/0.440
2w1hL0FCyclin-dependent kinase 22.7.11.220.440
3a9wNADNDP-sugar epimerase/0.440
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3le62BZCyclin-dependent kinase 22.7.11.220.440
3qqkX02Cyclin-dependent kinase 22.7.11.220.440
3qtrX36Cyclin-dependent kinase 22.7.11.220.440
3vrwYS5Vitamin D3 receptor/0.440
4a9hTVPBromodomain-containing protein 2/0.440
4axdANPInositol-pentakisphosphate 2-kinase2.7.1.1580.440
4b1fKRHGlutamate racemase/0.440
4eji0QACytochrome P450 2A131.14.14.10.440
4hgs15GCasein kinase I isoform gamma-32.7.11.10.440
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.440
4ylhYE1(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase/0.440
5iubCLRAdenosine receptor A2a/0.440