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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
1v59NADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1v59NADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.41.000
1zy8FADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.551
1zmcNADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.546
3ictFADCoenzyme A disulfide reductase/0.498
1ojtFADDihydrolipoyl dehydrogenase/0.496
2vn0TDZCytochrome P450 2C8/0.490
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.490
4r20AERCytochrome P450 family 17 polypeptide 2/0.488
1jioDEB6-deoxyerythronolide B hydroxylase/0.482
3zuyTCHTransporter/0.482
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.480
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.479
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.478
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.477
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.477
3s1dZIRCytokinin dehydrogenase 11.5.99.120.477
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.473
4tuvCPZCytochrome P450 1191.140.472
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.471
1eupASD6-deoxyerythronolide B hydroxylase/0.471
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.471
3gwfFADCyclohexanone monooxygenase/0.470
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
2nniMTKCytochrome P450 2C8/0.469
4cp4CAMCamphor 5-monooxygenase1.14.15.10.469
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.469
1jipKTN6-deoxyerythronolide B hydroxylase/0.468
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.468
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.468
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.467
4h3c0YZDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.467
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.467
1jpaANPEphrin type-B receptor 22.7.10.10.466
2cppCAMCamphor 5-monooxygenase1.14.15.10.466
2rhrEMOPutative ketoacyl reductase1.3.10.466
3icsADPCoenzyme A disulfide reductase/0.466
1enzNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.465
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.465
2ath3EAPeroxisome proliferator-activated receptor gamma/0.465
3cppCAMCamphor 5-monooxygenase1.14.15.10.465
4q72FADBifunctional protein PutA/0.465
1iwjCAMCamphor 5-monooxygenase1.14.15.10.464
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.464
1nzdUPGDNA beta-glucosyltransferase/0.464
1wntNAPL-xylulose reductase1.1.1.100.464
2ou2ACOHistone acetyltransferase KAT5/0.464
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
4q73FADBifunctional protein PutA/0.464
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.463
2rabNADGlutathione amide reductase/0.463
3u9eCOALmo1369 protein/0.463
3vt7VDXVitamin D3 receptor/0.463
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.463
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1dirNADDihydropteridine reductase1.5.1.340.462
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
3gobHXXDdmC/0.462
1dyhDZFDihydrofolate reductase1.5.1.30.461
2drcMTXDihydrofolate reductase1.5.1.30.461
3nr4PYVAbscisic acid receptor PYL2/0.461
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1pjcNADAlanine dehydrogenase/0.460
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.460
4l4cCAMCamphor 5-monooxygenase1.14.15.10.460
1kfbIGPTryptophan synthase alpha chain/0.459
1rj6AZMCarbonic anhydrase 144.2.1.10.459
1u28NADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.459
2y4gTIRTamL/0.459
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.459
4kne1CYDihydrofolate reductase1.5.1.30.459
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
2gjlFMNNitronate monooxygenase1.13.12.160.458
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.458
3lqfNADGalactitol dehydrogenase/0.458
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.458
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
4cdmFADDeoxyribodipyrimidine photolyase/0.458
5e8wSTUTGF-beta receptor type-12.7.11.300.458
1ez4NADL-lactate dehydrogenase1.1.1.270.457
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.457
1oc1ASVIsopenicillin N synthase1.21.3.10.457
1phgMYTCamphor 5-monooxygenase1.14.15.10.457
3kpkFADSulfide-quinone reductase/0.457
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
4n6hEJ4Delta-type opioid receptor/0.457
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.457
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.457
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
2a94AP0L-lactate dehydrogenase1.1.1.270.456
2ejvNADL-threonine 3-dehydrogenase/0.456
3uylTYDProbable NDP-rhamnosyltransferase/0.456
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
2y3rTRKTamL/0.455
3cmcNADGlyceraldehyde-3-phosphate dehydrogenase/0.455
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.455
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
1j39UPGDNA beta-glucosyltransferase/0.454
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.454
2givACOHistone acetyltransferase KAT8/0.454
3vt8YI3Vitamin D3 receptor/0.454
3vt9YI4Vitamin D3 receptor/0.454
3zkyWT4Isopenicillin N synthase1.21.3.10.454
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.454
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
4lxhC1EAlpha/beta hydrolase fold/0.454
5c88COAN-alpha-acetyltransferase/0.454
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.453
2oorNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.453
3a1nNADNDP-sugar epimerase/0.453
1dhjMTXDihydrofolate reductase1.5.1.30.452
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
1np7FADCryptochrome DASH/0.452
3cgeNDPCoenzyme A disulfide reductase/0.452
3mdvCL6Cholesterol 24-hydroxylase/0.452
3qlrNDPDihydrofolate reductase1.5.1.30.452
4g48PZBMycocyclosin synthase1.14.21.90.452
1mj9COAHistone acetyltransferase ESA1/0.451
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.451
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.451
2wdzNADGalactitol dehydrogenase/0.451
3nmpPYVAbscisic acid receptor PYL2/0.451
3qt62P0Mevalonate diphosphate decarboxylase/0.451
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1bwsNDPGDP-L-fucose synthase/0.450
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.450
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1kzjCB3Thymidylate synthase/0.450
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
2a7r5GPGMP reductase 2/0.450
2gjnFMNNitronate monooxygenase1.13.12.160.450
3cgcFADCoenzyme A disulfide reductase/0.450
3f5p741Insulin-like growth factor 1 receptor2.7.10.10.450
3nj0PYVAbscisic acid receptor PYL2/0.450
4xiwAZMCarbonic anhydrase, alpha type/0.450
1jmhUMPThymidylate synthase/0.449
1k6cMK1Gag-Pol polyprotein3.4.23.160.449
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.449
3fwiCAMCamphor 5-monooxygenase1.14.15.10.449
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.449
4i8vBHFCytochrome P450 1A11.14.14.10.449
4mihFADPyranose 2-oxidase1.1.3.100.449
1jolFFODihydrofolate reductase1.5.1.30.448
1re7FOLDihydrofolate reductase1.5.1.30.448
1t88CAMCamphor 5-monooxygenase1.14.15.10.448
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
2q5p241Peroxisome proliferator-activated receptor gamma/0.448
2q9fC3SCholesterol 24-hydroxylase/0.448
2x0iNAIMalate dehydrogenase/0.448
3vt3VDXVitamin D3 receptor/0.448
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4l4xNDPAmphI/0.448
4q71FADBifunctional protein PutA/0.448
1draMTXDihydrofolate reductase1.5.1.30.447
1hquHBYGag-Pol polyprotein2.7.7.490.447
1jg0DDTThymidylate synthase/0.447
1o6yACPSerine/threonine-protein kinase PknB2.7.11.10.447
1qvrANPChaperone protein ClpB/0.447
1t85CAMCamphor 5-monooxygenase1.14.15.10.447
2f1kNAPPrephenate dehydrogenase/0.447
2j4dFADCryptochrome DASH, chloroplastic/mitochondrial/0.447
2uxoTACHTH-type transcriptional regulator TtgR/0.447
3iaeD7KBenzaldehyde lyase/0.447
3koo24DBifunctional epoxide hydrolase 23.3.2.100.447
3vt65YIVitamin D3 receptor/0.447
3w0c6DSVitamin D3 receptor/0.447
4nmdFDABifunctional protein PutA/0.447
5akk1P8Bifunctional epoxide hydrolase 23.1.3.760.447
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.446
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.446
3qgtCP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.446
3zhbNAPPutative dehydrogenase/0.446
4k9dNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.446
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.446
5a3cNADSIR2 family protein/0.446
1gebCAMCamphor 5-monooxygenase1.14.15.10.445
1iwiCAMCamphor 5-monooxygenase1.14.15.10.445
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.445
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.445
2q59240Peroxisome proliferator-activated receptor gamma/0.445
3antS82Bifunctional epoxide hydrolase 23.3.2.100.445
3r5zF42Uncharacterized protein/0.445
3s79ASDAromatase1.14.14.140.445
3t2zFADSulfide-quinone reductase/0.445
3vrwYS5Vitamin D3 receptor/0.445
3zuxTCHTransporter/0.445
4bb3KKAIsopenicillin N synthase1.21.3.10.445
4l49CAMCamphor 5-monooxygenase1.14.15.10.445
4qecNAPElxO/0.445
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.445
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1dyjDDFDihydrofolate reductase1.5.1.30.444
1gcoNADGlucose 1-dehydrogenase1.1.1.470.444
1xny191Propionyl-CoA carboxylase complex B subunit/0.444
2cvwGDPRibonucleoside-diphosphate reductase large chain 11.17.4.10.444
2y3rTIRTamL/0.444
2zdt46CMitogen-activated protein kinase 102.7.11.240.444
3gxlQIGTGF-beta receptor type-12.7.11.300.444
3icrFADCoenzyme A disulfide reductase/0.444
3slkNDPPolyketide synthase extender module 2/0.444
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
4g3jVNTLanosterol 14-alpha-demethylase/0.444
4g47TZFMycocyclosin synthase1.14.21.90.444
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.444
4h4xFADBiphenyl dioxygenase ferredoxin reductase subunit/0.444
4hnc0UTMandelate racemase/0.444
4ienCOAPutative acyl-CoA hydrolase/0.444
4k6fNAPPutative Acetoacetyl-CoA reductase/0.444
4ktkKTKCytochrome P450/0.444
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.444
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
5a3bAPRSIR2 family protein/0.444
1fm4DXCMajor pollen allergen Bet v 1-L/0.443
1ia4TQ6Dihydrofolate reductase1.5.1.30.443
1lhwESMSex hormone-binding globulin/0.443
1xddAAYIntegrin alpha-L/0.443
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.443
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.443
3fwgCAMCamphor 5-monooxygenase1.14.15.10.443
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.443
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.443
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4h3ySAHtRNA (guanine-N(1)-)-methyltransferase/0.443
4m4922YL-lactate dehydrogenase A chain1.1.1.270.443
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.443
1u3dFADCryptochrome-1/0.442
2c3kABOSerine/threonine-protein kinase Chk12.7.11.10.442
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.442
3frqERYErythromycin resistance repressor protein/0.442
3oibFDAPutative acyl-CoA dehydrogenase/0.442
3uyk0CXProbable NDP-rhamnosyltransferase/0.442
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.442
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.442
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.442
4yswFADXanthine dehydrogenase/oxidase/0.442
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
2zawCAMCamphor 5-monooxygenase1.14.15.10.441
3b2eADPATPase GET3/0.441
3eqlMXPDNA-directed RNA polymerase subunit beta/0.441
3eqlMXPDNA-directed RNA polymerase subunit beta'/0.441
3r83Z14Cyclin-dependent kinase 22.7.11.220.441
4jdrFADDihydrolipoyl dehydrogenase1.8.1.40.441
5bsfNADPyrroline-5-carboxylate reductase/0.441
5cp4CAMCamphor 5-monooxygenase1.14.15.10.441
1blzACVIsopenicillin N synthase1.21.3.10.440
1m13HYFNuclear receptor subfamily 1 group I member 2/0.440
2fsvNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.440
2ignFADPyranose 2-oxidase/0.440
2iviACWIsopenicillin N synthase1.21.3.10.440
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.440
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.440
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3ns2PYVAbscisic acid receptor PYL2/0.440
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3to6LYS_CMCHistone acetyltransferase ESA1/0.440
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.440
4l4eCAMCamphor 5-monooxygenase1.14.15.10.440
4oqyNDP(S)-imine reductase/0.440