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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
1jcm137Tryptophan biosynthesis protein TrpCF4.1.1.48

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1jcm137Tryptophan biosynthesis protein TrpCF4.1.1.481.000
1towCRZFatty acid-binding protein, adipocyte/0.539
1touB1VFatty acid-binding protein, adipocyte/0.510
3fr4F8AFatty acid-binding protein, adipocyte/0.504
3fr28CAFatty acid-binding protein, adipocyte/0.501
4fhd0TTSpore photoproduct lyase/0.501
2xvv9DNSerum albumin/0.495
1u1f183Uridine phosphorylase2.4.2.30.493
1enpNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.492
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.488
2nnqT4BFatty acid-binding protein, adipocyte/0.487
3znrNU9Histone deacetylase 73.5.1.980.485
4h0yNADIota toxin component Ia/0.485
5stdUNNScytalone dehydratase4.2.1.940.485
1dgbNDPCatalase1.11.1.60.484
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.484
3l04SN0N-acetylornithine carbamoyltransferase2.1.3.90.481
4fkxCDPNucleoside diphosphate kinase/0.481
4rh10TTSpore photoproduct lyase/0.481
2vcmM11Isopenicillin N synthase1.21.3.10.480
3nmvPYVAbscisic acid receptor PYL2/0.480
3v0n4GWHisto-blood group ABO system transferase/0.480
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.479
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.479
3mauPLRPutative sphingosine-1-phosphate lyase/0.478
4bewACPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.478
4lzwTHMUridine phosphorylase/0.478
1cqp803Integrin alpha-L/0.476
1z0sATPNAD kinase/0.476
4du6GTPGTP cyclohydrolase 1/0.476
1pl6572Sorbitol dehydrogenase1.1.1.140.475
3fr5I4AFatty acid-binding protein, adipocyte/0.475
3ogwIMNLactoperoxidase1.11.1.70.475
1nceCB3Thymidylate synthase/0.473
2vbdV10Isopenicillin N synthase1.21.3.10.473
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.473
3iktNADRedox-sensing transcriptional repressor Rex/0.473
3pl8FADPyranose 2-oxidase/0.473
4lrrCF9Thymidylate synthase/0.473
1dghNDPCatalase1.11.1.60.472
1iayAVG1-aminocyclopropane-1-carboxylate synthase 24.4.1.140.472
2qhxFE1Pteridine reductase 11.5.1.330.472
3fpbATPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.472
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
4jhz1KVBeta-glucuronidase3.2.1.310.472
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.471
1nd52BFProstatic acid phosphatase3.1.3.20.471
1nj5P5AProline--tRNA ligase/0.471
3occDIHPurine nucleoside phosphorylase DeoD-type/0.471
3stdMQ0Scytalone dehydratase4.2.1.940.471
1vbiNADMalate/L-lactate dehydrogenase family protein/0.470
1yw8A75Methionine aminopeptidase 2/0.470
3l05SN0N-acetylornithine carbamoyltransferase2.1.3.90.470
4kbn25UDihydrofolate reductase1.5.1.30.470
1dr4HBIDihydrofolate reductase1.5.1.30.469
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.469
3tydXHPDihydropteroate synthase/0.468
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.468
1u1gBBBUridine phosphorylase2.4.2.30.467
2vbpVB1Isopenicillin N synthase1.21.3.10.467
3qvrFADGlucose oxidase1.1.3.40.467
4fhf0TTSpore photoproduct lyase/0.467
4uofDATNucleoside diphosphate kinase/0.467
3ungADPCRISPR system Cmr subunit Cmr2/0.466
1tojHCIAspartate aminotransferase2.6.1.10.465
3gieACPSensor histidine kinase DesK2.7.13.30.465
1qjfACSIsopenicillin N synthase1.21.3.10.464
3o9pMHIPeriplasmic murein peptide-binding protein/0.464
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.463
3fgoACPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.463
3nxoD2BDihydrofolate reductase1.5.1.30.463
3rl35GPMetallophosphoesterase MPPED23.10.463
4gqkADPActin cross-linking toxin VgrG1/0.463
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3l06SN0N-acetylornithine carbamoyltransferase2.1.3.90.462
3zoiM2WIsopenicillin N synthase1.21.3.10.462
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.461
4uohADPNucleoside diphosphate kinase/0.461
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.460
1wbbADPDNA mismatch repair protein MutS/0.460
2rd2QSIGlutamine--tRNA ligase6.1.1.180.460
1obnASVIsopenicillin N synthase1.21.3.10.459
3p0fBAUUridine phosphorylase 22.4.2.30.459
3phcIM5Purine nucleoside phosphorylase/0.459
3sl2ATPSensor histidine kinase WalK/0.459
4kf1HT5Aryldialkylphosphatase3.1.8.10.459
1e2lTMCThymidine kinase/0.458
1gpeFADGlucose oxidase1.1.3.40.458
2o8bADPDNA mismatch repair protein Msh2/0.458
2r2mI50Prothrombin3.4.21.50.458
2zsiGA4Gibberellin receptor GID1A30.458
4isuIKMGlutamate receptor 2/0.458
1n71COAAac(6')-Ii protein/0.457
1wuq8GTGTP cyclohydrolase 1/0.457
2bjsACVIsopenicillin N synthase1.21.3.10.457
2vczVC3Hematopoietic prostaglandin D synthase/0.457
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.457
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.457
1n3sGTPGTP cyclohydrolase 13.5.4.160.456
1yw7A41Methionine aminopeptidase 2/0.456
3c36KAIGlutamate receptor ionotropic, kainate 1/0.456
3phiNDPShikimate dehydrogenase (NADP(+))/0.456
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
5hpyGDPTransforming protein RhoA/0.456
1e2jTHMThymidine kinase/0.455
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.455
2uuoLK3UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.455
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.455
1be4PCGNucleoside diphosphate kinase A 22.7.4.60.454
1bk0ACVIsopenicillin N synthase1.21.3.10.454
1el4CTZObelin/0.454
1hb3SCVIsopenicillin N synthase1.21.3.10.454
1if6FBUCarbonic anhydrase 24.2.1.10.454
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.454
1qtqQSIGlutamine--tRNA ligase6.1.1.180.454
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.454
2wo7ASVIsopenicillin N synthase1.21.3.10.454
3wv9FEGHmd co-occurring protein HcgE/0.454
1dggNDPCatalase1.11.1.60.453
2cjeDUNDUTPase/0.453
2g78REACellular retinoic acid-binding protein 2/0.453
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2re8GSUGlutamine--tRNA ligase6.1.1.180.453
3l3rOAGDihydrofolate reductase1.5.1.30.453
3njoPYVAbscisic acid receptor PYR1/0.453
4a2aATPCell division protein FtsA/0.453
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
4kfj1R0Dihydrofolate reductase1.5.1.30.453
1hb1OCVIsopenicillin N synthase1.21.3.10.452
2pauD5M5'-deoxynucleotidase YfbR/0.452
2qo9ANPEphrin type-A receptor 32.7.10.10.452
3djfBC3Purine nucleoside phosphorylase/0.452
3kxoKXOHematopoietic prostaglandin D synthase/0.452
3lthUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.452
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4fa60TAPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.452
3emlZMAAdenosine receptor A2a/0.452
3gi2GHWDihydrofolate reductase1.5.1.30.451
1hfrMOTDihydrofolate reductase1.5.1.30.450
1kmyBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.450
1kzjCB3Thymidylate synthase/0.450
2bu9HFVIsopenicillin N synthase1.21.3.10.450
2iviACWIsopenicillin N synthase1.21.3.10.450
3ba6AN2Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.450
3nw3MU2Peptidoglycan recognition protein 1/0.450
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.450
4gukP2GNeuronal calcium sensor 1/0.450
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.449
1f5fDHTSex hormone-binding globulin/0.449
2dhfDZFDihydrofolate reductase1.5.1.30.449
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
3kzoAN0N-acetylornithine carbamoyltransferase2.1.3.90.449
4ap1NAPSteroid monooxygenase/0.449
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.449
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.449
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
5cuqNSCGenome polyprotein/0.449
1gky5GPGuanylate kinase2.7.4.80.448
1kqwRTLCellular retinol-binding protein type II/0.448
1toiHCIAspartate aminotransferase2.6.1.10.448
1w0kADPATP synthase subunit alpha, mitochondrial/0.448
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.448
3fhxPXLPyridoxal kinase2.7.1.350.448
3rc7TLOSugar 3-ketoreductase/0.448
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
4dlcUMPDeoxyuridine triphosphatase, putative/0.448
4qa0SHHHistone deacetylase 83.5.1.980.448
1a8t061Metallo-beta-lactamase type 2/0.447
1ahgTYR_PLPAspartate aminotransferase2.6.1.10.447
1vhnFMNtRNA-dihydrouridine synthase/0.447
1y56FMNUncharacterized protein/0.447
1y56FMN382aa long hypothetical sarcosine oxidase/0.447
2w3aTOPDihydrofolate reductase1.5.1.30.447
3bbfGDPNucleoside diphosphate kinase B2.7.4.60.447
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.447
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.447
4ie0PD2Alpha-ketoglutarate-dependent dioxygenase FTO/0.447
4jxxATPGlutamine--tRNA ligase6.1.1.180.447
4kebFOLDihydrofolate reductase1.5.1.30.447
1u1cBAUUridine phosphorylase2.4.2.30.446
1y1rANUUridine phosphorylase2.4.2.30.446
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.446
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.446
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.446
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.446
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3nmpPYVAbscisic acid receptor PYL2/0.446
3nxtD2EDihydrofolate reductase1.5.1.30.446
4cdmFO1Deoxyribodipyrimidine photolyase/0.446
4kak06UDihydrofolate reductase1.5.1.30.446
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.446
1i5aACPChemotaxis protein CheA2.7.13.30.445
1jx0DFVChalcone--flavonone isomerase 15.5.1.60.445
1mdlRMNMandelate racemase/0.445
1qiqACCIsopenicillin N synthase1.21.3.10.445
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.445
2an9GDPGuanylate kinase2.7.4.80.445
2zytPPSSulfotransferase 1 family member D1/0.445
3ahiHTLProbable phosphoketolase/0.445
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.445
3h3sH15Collagen type IV alpha-3-binding protein/0.445
3nbwTR4Ketohexokinase/0.445
3ntgD72Prostaglandin G/H synthase 21.14.99.10.445
5c4cUPGHisto-blood group ABO system transferase/0.445
5k2aZMAAdenosine receptor A2a/0.445
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.444
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1if5FBTCarbonic anhydrase 24.2.1.10.444
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
3ewkFADSensory box histidine kinase/response regulator/0.444
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4qnvGEKtRNA U34 carboxymethyltransferase/0.444
4xw5ATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
4ytnFD8Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.444
4ytnFD8Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial/0.444
4ytnFD8Succinate dehydrogenase cytochrome b560/0.444
1a9cGTPGTP cyclohydrolase 13.5.4.160.443
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.443
1mdlSMNMandelate racemase/0.443
1n5vNOMActVA 6 protein/0.443
1synF89Thymidylate synthase/0.443
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.443
2rlcCHDCholoylglycine hydrolase3.5.1.240.443
3gcq1BUMitogen-activated protein kinase 14/0.443
3h4vNAPPteridine reductase 11.5.1.330.443
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4fs4H24Beta-secretase 13.4.23.460.443
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
1p4aPCPPur operon repressor/0.442
1pd9CO4Dihydrofolate reductase1.5.1.30.442
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2rqfJH3Hemolymph juvenile hormone binding protein/0.442
3apwDP0Alpha-1-acid glycoprotein 2/0.442
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4a0sCO8Octenoyl-CoA reductase/carboxylase/0.442
4adcPLPSuccinylornithine transaminase2.6.1.810.442
4j4vSVRNucleocapsid protein/0.442
4l2zS7MS-adenosylmethionine synthase/0.442
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
5jtbZMAAdenosine receptor A2a/0.442
1je1GMPPurine nucleoside phosphorylase/0.441
1nm6L86Prothrombin3.4.21.50.441
1pq6965Oxysterols receptor LXR-beta/0.441
2bakAQZMitogen-activated protein kinase 14/0.441
2ewaSB2Mitogen-activated protein kinase 14/0.441
2q0gUPUPoly(A) polymerase, putative/0.441
3ed1GA3Gibberellin receptor GID1/0.441
3fowIMHPurine nucleoside phosphorylase/0.441
3nf8CDQGag-Pol polyprotein/0.441
3zy3GDPGDP-fucose protein O-fucosyltransferase 12.4.1.2210.441
4a9yAQZMitogen-activated protein kinase 14/0.441
4ha6PXMPyridoxine 4-oxidase/0.441
4kc1WS1Histo-blood group ABO system transferase/0.441
4n4v2GYTankyrase-12.4.2.300.441
4stdBFSScytalone dehydratase4.2.1.940.441
1cjvDADAdenylate cyclase type 2/0.440
1cjvDADAdenylate cyclase type 5/0.440
1g7vPAI2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.440
1gwrESTEstrogen receptor/0.440
1kquBR4Phospholipase A2, membrane associated/0.440
1lwxAZDNucleoside diphosphate kinase, cytosolic2.7.4.60.440
1qv0CZHObelin/0.440
1rxjBNIStreptavidin/0.440
1stoOMPOrotate phosphoribosyltransferase/0.440
2jlaTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.440
2nliFMNLactate oxidase/0.440
2q6hCXXNa(+):neurotransmitter symporter (Snf family)/0.440
2xvq9DSSerum albumin/0.440
3bgxTMPThymidylate synthase/0.440
3nxrD2DDihydrofolate reductase1.5.1.30.440
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4f6w0SSCyclin-dependent kinase 82.7.11.220.440
4ku2MYA3-oxoacyl-[ACP] synthase III/0.440
4rp8ASCAscorbate-specific PTS system EIIC component/0.440