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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
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.21.000
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.647
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.646
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.619
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.602
3icrCOACoenzyme A disulfide reductase/0.501
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.494
3vt7VDXVitamin D3 receptor/0.494
3icsCOACoenzyme A disulfide reductase/0.486
4q71FADBifunctional protein PutA/0.486
2wesFADTryptophan 5-halogenase/0.485
3ictADPCoenzyme A disulfide reductase/0.485
5k2cZMAAdenosine receptor A2a/0.485
1yb5NAPQuinone oxidoreductase1.6.5.50.482
3ictCOACoenzyme A disulfide reductase/0.482
3vt9YI4Vitamin D3 receptor/0.482
3nxxNDPDihydrofolate reductase1.5.1.30.481
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.480
3vt8YI3Vitamin D3 receptor/0.480
3cgfJNFMitogen-activated protein kinase 102.7.11.240.478
4iaq2GM5-hydroxytryptamine receptor 1B/0.478
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.475
5k2aZMAAdenosine receptor A2a/0.475
1lriCLRBeta-elicitin cryptogein/0.473
3ua506XCytochrome P450 2B61.14.130.473
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.472
3r5yF42Uncharacterized protein/0.472
5jlaNADPutative short-chain dehydrogenase/reductase/0.471
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.470
1osvCHCBile acid receptor/0.470
1ot7CHCBile acid receptor/0.470
4g1z0VPVitamin D3 receptor A/0.470
2p33J07Mitogen-activated protein kinase 102.7.11.240.469
2b9wFADPutative aminooxidase/0.468
3sgx0FWDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.468
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.468
3d84NDPDihydrofolate reductase1.5.1.30.466
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.466
3kpkFADSulfide-quinone reductase/0.465
3t2kFADSulfide-quinone reductase/0.465
3tqhNDPQuinone oxidoreductase/0.465
5k2bZMAAdenosine receptor A2a/0.465
1jioDEB6-deoxyerythronolide B hydroxylase/0.464
1yinCM3Estrogen receptor/0.464
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.464
3w18N13Aurora kinase A2.7.11.10.464
4eevL1XHepatocyte growth factor receptor2.7.10.10.464
1fwkADPHomoserine kinase2.7.1.390.463
1jpaANPEphrin type-B receptor 22.7.10.10.463
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.463
2znnS44Peroxisome proliferator-activated receptor alpha/0.463
3cv9VDXVitamin D3 dihydroxylase/0.463
3t2zFADSulfide-quinone reductase/0.463
3vtcTK3Vitamin D3 receptor/0.463
4iarERM5-hydroxytryptamine receptor 1B/0.463
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3lqfNADGalactitol dehydrogenase/0.462
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.462
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.462
4kwhNAPReductase homolog/0.462
4otwDB8Receptor tyrosine-protein kinase erbB-32.7.10.10.462
1y4lSVRBasic phospholipase A2 homolog 2/0.461
2bhiSFTCytotoxin 3/0.461
2q9fC3SCholesterol 24-hydroxylase/0.461
3atzFMNProstaglandin F2a synthase/0.461
3d4pNADL-lactate dehydrogenase 11.1.1.270.461
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
3mqe416Prostaglandin G/H synthase 21.14.99.10.461
3oafOAGDihydrofolate reductase1.5.1.30.461
2po7CHDFerrochelatase, mitochondrial4.99.1.10.460
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.460
3qlrNDPDihydrofolate reductase1.5.1.30.460
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
5jtbZMAAdenosine receptor A2a/0.460
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
1t0lNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.459
1tj0FADBifunctional protein PutA1.5.5.20.459
2zb3NDPProstaglandin reductase 21.3.1.480.459
3b6zCO7Enoyl reductase LovC10.459
3cgoJNOMitogen-activated protein kinase 102.7.11.240.459
3t2yFADSulfide-quinone reductase/0.459
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.459
4ez72ANCyclin-dependent kinase 22.7.11.220.459
4kl9NDPDihydrofolate reductase1.5.1.30.459
4tuvCPZCytochrome P450 1191.140.459
1f4fTP3Thymidylate synthase/0.458
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.458
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.458
2x9dITCTetracycline repressor protein class D/0.458
2z3uCRRCytochrome P450/0.458
3f69XDRSerine/threonine-protein kinase PknB2.7.11.10.458
3icsADPCoenzyme A disulfide reductase/0.458
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.458
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.458
3vt5YI2Vitamin D3 receptor/0.458
4enhFVXCholesterol 24-hydroxylase/0.458
4pd6URINucleoside permease/0.458
1njfAGSDNA polymerase III subunit tau2.7.7.70.457
2zbzVDXVitamin D3 dihydroxylase/0.457
4ijp1EHSerine/threonine-protein kinase PRP4 homolog2.7.11.10.457
1fmlRTLRetinol dehydratase/0.456
1og5SWFCytochrome P450 2C9/0.456
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
2wetFADTryptophan 5-halogenase/0.456
4hnc0UTMandelate racemase/0.456
4nb6444Nuclear receptor ROR-gamma/0.456
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.455
2y05NAPProstaglandin reductase 1/0.455
3mdmFJZCholesterol 24-hydroxylase/0.455
3mdvCL6Cholesterol 24-hydroxylase/0.455
3pe6ZYHMonoglyceride lipase/0.455
4dit0KDGlycogen synthase kinase-3 beta2.7.11.260.455
4ia7BIVVitamin D3 receptor A/0.455
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
1rbzKT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.454
3l8p0CEAngiopoietin-1 receptor2.7.10.10.454
3ttjJBIMitogen-activated protein kinase 102.7.11.240.454
4cd2FOLDihydrofolate reductase1.5.1.30.454
4q73FADBifunctional protein PutA/0.454
4ryvZEAProtein LlR18A/0.454
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.453
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.453
2y3rTRKTamL/0.453
3bfb9ODPheromone-binding protein ASP1/0.453
3och2MXDihydrofolate reductase1.5.1.30.453
4nc3ERM5-hydroxytryptamine receptor 2B/0.453
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1sn5T3Transthyretin/0.452
2hw2RFPRifampin ADP-ribosyl transferase/0.452
2y9qANPMitogen-activated protein kinase 12.7.11.240.452
3iaeD7KBenzaldehyde lyase/0.452
3zuyTCHTransporter/0.452
1dkfBMSRetinoic acid receptor alpha/0.451
1ppjANYCytochrome b/0.451
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.451
1tw4CHDFatty acid-binding protein, liver/0.451
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.451
4cy8FDA2-hydroxybiphenyl-3-monooxygenase/0.451
4ia1BIVVitamin D3 receptor A/0.451
4y8wSTRSteroid 21-hydroxylase/0.451
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.450
1ml6GBXGlutathione S-transferase A22.5.1.180.450
1qorNDPQuinone oxidoreductase 1/0.450
2yirYIRSerine/threonine-protein kinase Chk22.7.11.10.450
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.450
3qlsNDPDihydrofolate reductase1.5.1.30.450
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.450
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
1dajMOTDihydrofolate reductase1.5.1.30.449
1ikvEFZGag-Pol polyprotein2.7.7.490.449
1v9aSAHUncharacterized protein/0.449
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.449
2nomDUTPoly(A) polymerase, putative/0.449
2q5g1FAPeroxisome proliferator-activated receptor delta/0.449
2zawCAMCamphor 5-monooxygenase1.14.15.10.449
3gwfFADCyclohexanone monooxygenase/0.449
3inmNDPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.449
3sz0FADSulfide-quinone reductase/0.449
3uleC69Actin-related protein 3/0.449
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.449
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.449
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.449
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.449
1a27ESTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
1qxlFR8Adenosine deaminase3.5.4.40.448
1u28NADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.448
1zg32HIIsoflavone 4'-O-methyltransferase/0.448
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
2j5xGSPADP-ribosylation factor 6/0.448
2obyNAPQuinone oxidoreductase PIG310.448
2ydvNECAdenosine receptor A2a/0.448
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3oqkS52Renin3.4.23.150.448
4tvbNADHomospermidine synthase2.5.1.440.448
4xiwAZMCarbonic anhydrase, alpha type/0.448
5j4eFMNSensory box protein/0.448
1m78NDPDihydrofolate reductase1.5.1.30.447
1rx1NAPDihydrofolate reductase1.5.1.30.447
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.447
2wqeADPAurora kinase A2.7.11.10.447
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.447
3h1jSMACytochrome b/0.447
3n0hTOPDihydrofolate reductase1.5.1.30.447
3wmxNADNAD dependent epimerase/dehydratase/0.447
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.447
4eiyZMAAdenosine receptor A2a/0.447
4xumIMNPeroxisome proliferator-activated receptor gamma/0.447
5eccNAPDehydrofolate reductase type I/0.447
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1qvnFRIInterleukin-2/0.446
1r2jFADFkbI/0.446
2zlaVDBVitamin D3 receptor/0.446
3hl0NADMaleylacetate reductase/0.446
3oibFDAPutative acyl-CoA dehydrogenase/0.446
3oriAGSSerine/threonine protein kinase/0.446
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.446
3zk5Z18Cytochrome P450 monooxygenase PikC/0.446
4bb3KKAIsopenicillin N synthase1.21.3.10.446
4jufTPPBenzoylformate decarboxylase4.1.1.70.446
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.446
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4yt5H4MH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338/0.446
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
4z9g1Q5Corticotropin-releasing factor receptor 1/0.446
1knuYPAPeroxisome proliferator-activated receptor gamma/0.445
1rx7FOLDihydrofolate reductase1.5.1.30.445
1zeoC01Peroxisome proliferator-activated receptor gamma/0.445
2cmvNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.445
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.445
2p4yC03Peroxisome proliferator-activated receptor gamma/0.445
2ydoADNAdenosine receptor A2a/0.445
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3fr0AJBGlucokinase2.7.1.20.445
3jynNDPQuinone oxidoreductase/0.445
4fehFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.445
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.445
4k9u5AWCytochrome P450 3A4/0.445
4knzCB3Thymidylate synthase/0.445
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.445
4zasTYDCalS13/0.445
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.444
1eioGCHGastrotropin/0.444
1k6pXN3Gag-Pol polyprotein3.4.23.160.444
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.444
2hziJINTyrosine-protein kinase ABL12.7.10.20.444
2jn3JN3Fatty acid-binding protein, liver/0.444
2w9hTOPDihydrofolate reductase1.5.1.30.444
2ylrFADPhenylacetone monooxygenase1.14.13.920.444
3b20NADGlyceraldehyde-3-phosphate dehydrogenase/0.444
3gqvNAPEnoyl reductase LovC10.444
3s7a684Dihydrofolate reductase1.5.1.30.444
4gah0ETAcyl-coenzyme A thioesterase THEM43.1.2.20.444
4ia2BIVVitamin D3 receptor A/0.444
4qi5FADCellobiose dehydrogenase/0.444
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.444
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
1t88CAMCamphor 5-monooxygenase1.14.15.10.443
1w4zNAPPutative ketoacyl reductase1.3.10.443
2ardFDAFlavin-dependent tryptophan halogenase PrnA1.14.19.90.443
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.443
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2ok7FADFerredoxin--NADP reductase, apicoplast/0.443
2ycqUPXSerine/threonine-protein kinase Chk22.7.11.10.443
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.443
3eej53RUncharacterized protein/0.443
3hazFADBifunctional protein PutA/0.443
3ijdC2FMethylenetetrahydrofolate reductase/0.443
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3syiFADSulfide-quinone reductase/0.443
3tqaNDPDihydrofolate reductase/0.443
3vrwYS5Vitamin D3 receptor/0.443
3vt45YIVitamin D3 receptor/0.443
3w0hW12Vitamin D3 receptor/0.443
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.443
5awmANPStress-activated protein kinase JNK2.7.11.240.443
5iua6DXAdenosine receptor A2a/0.443
1bygSTUTyrosine-protein kinase CSK/0.442
1fmjRTLRetinol dehydratase/0.442
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
2c0cNAPProstaglandin reductase 310.442
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.442
2wsbNADGalactitol dehydrogenase/0.442
2y30SM8Putative repressor SimReg2/0.442
3e2sFADBifunctional protein PutA1.5.5.20.442
3ns2PYVAbscisic acid receptor PYL2/0.442
3t14FADSulfide-quinone reductase/0.442
3to6LYS_CMCHistone acetyltransferase ESA1/0.442
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.442
3w33W19Epidermal growth factor receptor2.7.10.10.442
4dfrMTXDihydrofolate reductase1.5.1.30.442
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.442
4ia3BIVVitamin D3 receptor A/0.442
4rujVDXVitamin D3 receptor A/0.442
4ruoBIVVitamin D3 receptor A/0.442
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1ai9NDPDihydrofolate reductase1.5.1.30.441
1dr5NAPDihydrofolate reductase1.5.1.30.441
2ca0PXICytochrome P450 monooxygenase PikC/0.441
2cig1DGDihydrofolate reductase1.5.1.30.441
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.441
2yitYITSerine/threonine-protein kinase Chk22.7.11.10.441
3a60STURibosomal protein S6 kinase beta-12.7.11.10.441
3drcMTXDihydrofolate reductase1.5.1.30.441
3i0rRT3Gag-Pol polyprotein2.7.7.490.441
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.441
3nbwTR4Ketohexokinase/0.441
3s1dZIRCytokinin dehydrogenase 11.5.99.120.441
3up3XCAaceDAF-12/0.441
4bi1ZO6Dual specificity protein kinase TTK2.7.12.10.441
4l425FIRibosomal protein S6 kinase beta-12.7.11.10.441
4lb2DM5Serum albumin/0.441
4lxhC1EAlpha/beta hydrolase fold/0.441
4mihFADPyranose 2-oxidase1.1.3.100.441
4uhrNGIAdenosine receptor A2a/0.441
1f123HCHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
1gebCAMCamphor 5-monooxygenase1.14.15.10.440
1k6tXN1Gag-Pol polyprotein3.4.23.160.440
1mrwK57Gag-Pol polyprotein3.4.23.160.440
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
1uyrD1LAcetyl-CoA carboxylase/0.440
1w1rZEACytokinin dehydrogenase 11.5.99.120.440
1xkkFMMEpidermal growth factor receptor2.7.10.10.440
2ar8FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.440
2j3iNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.440
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.440
3pgqGY3Acetyl-CoA carboxylase/0.440
3vt3VDXVitamin D3 receptor/0.440
4ctaATPCinA-like protein/0.440
4ejmNAPPutative zinc-binding dehydrogenase/0.440
4h50NAPBiphenyl dioxygenase ferredoxin reductase subunit/0.440
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4j6dTESCytochrome P450 monooxygenase/0.440
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.440
4q72FADBifunctional protein PutA/0.440
4xq9NADHomospermidine synthase2.5.1.440.440
4y95746Tyrosine-protein kinase/0.440
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.440
5envNADAlcohol dehydrogenase 11.1.1.10.440
3emlZMAAdenosine receptor A2a/0.440