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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
4cokTPPPyruvate decarboxylase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4cokTPPPyruvate decarboxylase/1.000
4zp1TPPPyruvate decarboxylase4.1.1.10.646
1qpbTPPPyruvate decarboxylase isozyme 1/0.613
1ovmTPPIndole-3-pyruvate decarboxylase4.1.1.740.592
3oe1TDLPyruvate decarboxylase4.1.1.10.582
2vk4TPPPyruvate decarboxylase4.1.1.10.578
2w93TPPPyruvate decarboxylase isozyme 1/0.572
2vk8TPPPyruvate decarboxylase isozyme 1/0.570
2q5oPPYIndole-3-pyruvate decarboxylase4.1.1.740.525
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.523
2ag0TPPBenzaldehyde lyase/0.521
2q5oTPWIndole-3-pyruvate decarboxylase4.1.1.740.507
1ozhHE3Acetolactate synthase, catabolic2.2.1.60.493
1y9dTPPPyruvate oxidase1.2.3.30.491
2c42TPPPyruvate synthase/0.490
3i2834NBifunctional epoxide hydrolase 23.3.2.100.489
2c3oTPPPyruvate synthase/0.488
4rtkSAHDNA adenine methylase2.1.1.720.488
4fqsLYAThymidylate synthase ThyA/0.485
1m78NDPDihydrofolate reductase1.5.1.30.483
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.480
2ihvTPPN(2)-(2-carboxyethyl)arginine synthase/0.480
2ihuTP9N(2)-(2-carboxyethyl)arginine synthase/0.477
4rtrSAMDNA adenine methylase2.1.1.720.476
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.475
4ez8DHFThymidylate synthase2.1.1.450.473
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.473
2xae2XAKinesin-like protein KIF11/0.472
3pjcPJCTyrosine-protein kinase JAK32.7.10.20.472
5exdTPPOxalate oxidoreductase subunit alpha/0.472
5exdTPPOxalate oxidoreductase subunit beta/0.472
2ag1TPPBenzaldehyde lyase/0.470
2panTDPGlyoxylate carboligase4.1.1.470.470
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.470
2v3wTPPBenzoylformate decarboxylase4.1.1.70.469
4hxs1A3Bromodomain-containing protein 4/0.469
5f2kSAHUncharacterized protein/0.469
1txzAPRProbable ADP-ribose 1''-phosphate phosphatase YML087W3.1.3.840.467
3gamMXXRibosyldihydronicotinamide dehydrogenase [quinone]/0.467
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.466
2ym7YM7Serine/threonine-protein kinase Chk12.7.11.10.466
1jm6ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.465
2np7NEAModification methylase TaqI2.1.1.720.465
2uz1TPPBenzaldehyde lyase/0.465
2ym5YM5Serine/threonine-protein kinase Chk12.7.11.10.465
3lw0CCXInsulin-like growth factor 1 receptor2.7.10.10.465
3rnoNAPNAD(P)H-hydrate epimerase5.1.99.60.465
2bbqPFGThymidylate synthase/0.464
2jlaTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.464
4jufTPPBenzoylformate decarboxylase4.1.1.70.464
4mobCOAAcyl-coenzyme A thioesterase 123.1.2.10.464
1svmATPLarge T antigen3.6.40.463
1synF89Thymidylate synthase/0.462
1qpePP2Tyrosine-protein kinase Lck2.7.10.20.461
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
2qhn582Serine/threonine-protein kinase Chk12.7.11.10.461
2bfmTOPPteridine reductase 11.5.1.330.460
3o6o94MHeat shock protein 83/0.460
3uxhUXHRibosyldihydronicotinamide dehydrogenase [quinone]/0.460
3wbbNAPMeso-diaminopimelate D-dehydrogenase/0.460
4zvmDM2Ribosyldihydronicotinamide dehydrogenase [quinone]/0.460
1fw0KAIGlutamate receptor 2/0.459
1itzTPPTransketolase, chloroplastic2.2.1.10.459
3nhjA2ZRibosyldihydronicotinamide dehydrogenase [quinone]/0.459
3nhlYTRRibosyldihydronicotinamide dehydrogenase [quinone]/0.459
1uu8BI13-phosphoinositide-dependent protein kinase 12.7.11.10.458
2hb7O1CVitamin D3 receptor/0.458
3o0iP54Heat shock protein HSP 90-alpha/0.458
2c3yHTLPyruvate synthase/0.457
2qg2A91Heat shock protein HSP 90-alpha/0.457
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.457
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.457
2vmyFFOSerine hydroxymethyltransferase/0.456
2x8eX8ESerine/threonine-protein kinase Chk12.7.11.10.456
3hz142CHeat shock protein HSP 90-alpha/0.456
4o71CPBBromodomain-containing protein 4/0.456
1drhNAPDihydrofolate reductase1.5.1.30.455
1hvyD16Thymidylate synthase2.1.1.450.455
2wugHPK4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.455
4cp4CAMCamphor 5-monooxygenase1.14.15.10.455
1jtqLY3Thymidylate synthase/0.454
3biz61EWee1-like protein kinase2.7.10.20.454
3nr4PYVAbscisic acid receptor PYL2/0.454
3s7a684Dihydrofolate reductase1.5.1.30.454
4rtsSAMDNA adenine methylase2.1.1.720.454
1agwSU2Fibroblast growth factor receptor 1/0.453
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.453
1kekHTLPyruvate synthase/0.453
1uy9PU6Heat shock protein HSP 90-alpha/0.453
2ohjFMNType A flavoprotein FprA10.453
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.453
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.453
3qbwADPAnhydro-N-acetylmuramic acid kinase/0.453
3u5sFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.453
4a5lNDPThioredoxin reductase/0.453
4kwi1TJReductase homolog/0.453
3qakUKAAdenosine receptor A2a/0.453
2c31ADPOxalyl-CoA decarboxylase4.1.1.80.452
2ftoTMPThymidylate synthase/0.452
3ddw055Glycogen phosphorylase, liver form2.4.1.10.452
4ffrATPUncharacterized protein/0.452
5cccDDFDihydrofolate reductase1.5.1.30.452
2fwzH71Heat shock protein HSP 90-alpha/0.451
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.451
3csdEMOPutative ketoacyl reductase1.3.10.451
3fwjCAMCamphor 5-monooxygenase1.14.15.10.451
3ggcH26Hypoxanthine-guanine phosphoribosyltransferase2.4.2.80.451
3v49PK0Androgen receptor/0.451
4bdcODHSerine/threonine-protein kinase Chk22.7.11.10.451
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.451
4k9nTZDBenzoylformate decarboxylase4.1.1.70.451
1axwMTXThymidylate synthase/0.450
1jujLYAThymidylate synthase2.1.1.450.450
1zosMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.450
2h55DZ8Heat shock protein HSP 90-alpha/0.450
2p5uNADUDP-glucose 4-epimerase/0.450
2yeiXQIHeat shock protein HSP 90-alpha/0.450
2z97CAMCamphor 5-monooxygenase1.14.15.10.450
3k4551PDihydrofolate reductase1.5.1.30.450
4c04SFGProtein arginine N-methyltransferase 6/0.450
4lyw21QBromodomain-containing protein 4/0.450
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.449
1tduCB3Thymidylate synthase/0.449
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.449
4fwfFADLysine-specific histone demethylase 1B10.449
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.449
4z1fH71Heat shock protein 75 kDa, mitochondrial/0.449
5bukFADFADH2-dependent halogenase/0.449
1jtuLYBThymidylate synthase/0.448
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.448
2hasC3OVitamin D3 receptor/0.448
2hb8MVDVitamin D3 receptor/0.448
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.448
3hz137DHeat shock protein HSP 90-alpha/0.448
4aw0ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.448
4twnB96Ephrin type-A receptor 32.7.10.10.448
1jayF42F420-dependent NADP reductase/0.447
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
1uyuCAMCamphor 5-monooxygenase1.14.15.10.447
1y4sADPChaperone protein HtpG/0.447
1zcbGDPGuanine nucleotide-binding protein subunit alpha-13/0.447
2ftoCB3Thymidylate synthase/0.447
2przOMPOrotate phosphoribosyltransferase 12.4.2.100.447
2zfnACOHistone acetyltransferase RTT1092.3.1.480.447
3ggj25HHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.447
3jq8DX3Pteridine reductase, putative/0.447
3qh23NMThiazole tautomerase/0.447
3wznBTNStreptavidin/0.447
4deg0JJHepatocyte growth factor receptor2.7.10.10.447
4qnaX11Serine/threonine-protein kinase 242.7.11.10.447
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
7catNDPCatalase1.11.1.60.447
2jibTPPOxalyl-CoA decarboxylase4.1.1.80.446
2ym2FADPhenylacetone monooxygenase1.14.13.920.446
2ym3YM3Serine/threonine-protein kinase Chk12.7.11.10.446
3nhuM42Ribosyldihydronicotinamide dehydrogenase [quinone]/0.446
4nyv15ECREB-binding protein/0.446
1kbiFMNCytochrome b2, mitochondrial1.1.2.30.445
1rk3VDXVitamin D3 receptor/0.445
1szcCNANAD-dependent protein deacetylase HST23.5.10.445
1uy7PU4Heat shock protein HSP 90-alpha/0.445
1vhnFMNtRNA-dihydrouridine synthase/0.445
2hamC33Vitamin D3 receptor/0.445
2q5qKPVIndole-3-pyruvate decarboxylase4.1.1.740.445
2z3uCRRCytochrome P450/0.445
3ac1KZITyrosine-protein kinase Lck2.7.10.20.445
3bbfGDPNucleoside diphosphate kinase B2.7.4.60.445
3zptM8YGag-Pol polyprotein3.4.23.160.445
4at0FADPossible succinate dehydrogenase/0.445
4fswHK6Serine/threonine-protein kinase Chk12.7.11.10.445
4k9pTPPBenzoylformate decarboxylase4.1.1.70.445
5cyoGDPSeptin-9/0.445
5fuwTHMThymidine kinase, putative/0.445
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.444
1g67TZPThiamine-phosphate synthase/0.444
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.444
1uy8PU5Heat shock protein HSP 90-alpha/0.444
1uycPU7Heat shock protein HSP 90-alpha/0.444
2a1nCAMCamphor 5-monooxygenase1.14.15.10.444
2cppCAMCamphor 5-monooxygenase1.14.15.10.444
2g1pSAHDNA adenine methylase2.1.1.720.444
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.444
2vt4P32Beta-1 adrenergic receptor/0.444
3a20FMNFMN-binding protein/0.444
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.444
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.444
3ozrOZRCatechol O-methyltransferase2.1.1.60.444
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.444
4hy6FJ1Heat shock protein HSP 90-alpha/0.444
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.444
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.444
1uyePU9Heat shock protein HSP 90-alpha/0.443
1uyhPU0Heat shock protein HSP 90-alpha/0.443
3bgxMEFThymidylate synthase/0.443
3g2hKOTGlycogen phosphorylase, muscle form2.4.1.10.443
3kpzZNEVitamin D3 receptor/0.443
4h4rFADBiphenyl dioxygenase ferredoxin reductase subunit/0.443
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.443
4jlm1NNDeoxycytidine kinase2.7.1.740.443
4mryCEIObelin/0.443
4u7wNDPMxaA/0.443
1w2xRCPAcetyl-CoA carboxylase/0.442
2gs7ANPEpidermal growth factor receptor2.7.10.10.442
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.442
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.442
3cppCAMCamphor 5-monooxygenase1.14.15.10.442
4c67L5SBromodomain-containing protein 4/0.442
4dpy2P0Mevalonate diphosphate decarboxylase/0.442
4qmtH1NSerine/threonine-protein kinase 242.7.11.10.442
4rtjSFGDNA adenine methylase2.1.1.720.442
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
1h1wATP3-phosphoinositide-dependent protein kinase 12.7.11.10.441
2bunFADAppA protein/0.441
2uyqSAMPutative S-adenosyl-L-methionine-dependent methyltransferase ML26402.1.10.441
2ywvADPPhosphoribosylaminoimidazole-succinocarboxamide synthase/0.441
2zthSAMCatechol O-methyltransferase2.1.1.60.441
3mnrSD1Heat shock protein HSP 90-alpha/0.441
3q0vLL4HTH-type transcriptional regulator EthR/0.441
3q5iANPProtein kinase, putative/0.441
3qf9NM8Serine/threonine-protein kinase pim-12.7.11.10.441
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.441
4bqh9VUUDP-N-acetylglucosamine pyrophosphorylase, putative/0.441
4bvnP32Beta-1 adrenergic receptor/0.441
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.441
4qppSAHProtein arginine N-methyltransferase 6/0.441
5br7FADUDP-galactopyranose mutase/0.441
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.441
1crbRTLRetinol-binding protein 1/0.440
1phePIYCamphor 5-monooxygenase1.14.15.10.440
1s0zEB1Vitamin D3 receptor/0.440
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.440
2wmuZYUSerine/threonine-protein kinase Chk12.7.11.10.440
3cgcCOACoenzyme A disulfide reductase/0.440
4awq592Heat shock protein HSP 90-alpha/0.440
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.440
4ivrN50Thymidine kinase/0.440
4rtoSFGDNA adenine methylase2.1.1.720.440