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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
1cbsREACellular retinoic acid-binding protein 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1cbsREACellular retinoic acid-binding protein 2/1.000
2g78REACellular retinoic acid-binding protein 2/0.800
2cbsR13Cellular retinoic acid-binding protein 2/0.718
3cbsR12Cellular retinoic acid-binding protein 2/0.644
1cbrREACellular retinoic acid-binding protein 1/0.621
1cbqRE9Cellular retinoic acid-binding protein 2/0.589
3cwkREACellular retinoic acid-binding protein 2/0.556
2cbrA80Cellular retinoic acid-binding protein 1/0.534
2fr3REACellular retinoic acid-binding protein 2/0.526
1sozVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.507
1osvCHCBile acid receptor/0.503
1kzjCB3Thymidylate synthase/0.498
3t2zFADSulfide-quinone reductase/0.491
2om9AJAPeroxisome proliferator-activated receptor gamma/0.489
3jynNDPQuinone oxidoreductase/0.488
3tvuB37Acetyl-CoA carboxylase/0.488
1kkq471Peroxisome proliferator-activated receptor alpha/0.486
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.486
1ot7CHCBile acid receptor/0.481
1w2xRCPAcetyl-CoA carboxylase/0.481
3a1l2CCCytochrome P450/0.479
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.477
4nmdFDABifunctional protein PutA/0.474
1ppjSMACytochrome b/0.473
3kpkFADSulfide-quinone reductase/0.473
4xumIMNPeroxisome proliferator-activated receptor gamma/0.473
5hs1VORLanosterol 14-alpha demethylase/0.473
3qakUKAAdenosine receptor A2a/0.473
2hfpNSIPeroxisome proliferator-activated receptor gamma/0.472
2r3yVAL_TYR_TRP_PHESerine endoprotease DegS3.4.21.1070.472
3h0aD30Peroxisome proliferator-activated receptor gamma/0.472
4a2aATPCell division protein FtsA/0.472
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.472
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.472
1tl7ONMAdenylate cyclase type 2/0.470
1tl7ONMAdenylate cyclase type 5/0.470
3h0sB38Acetyl-CoA carboxylase/0.470
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.469
1fm4DXCMajor pollen allergen Bet v 1-L/0.468
1jipKTN6-deoxyerythronolide B hydroxylase/0.468
1pp9SMACytochrome b/0.468
3lu8IQXSerum albumin/0.468
3v9y24LPeroxisome proliferator-activated receptor gamma/0.468
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.467
4ia1BIVVitamin D3 receptor A/0.467
1qorNDPQuinone oxidoreductase 1/0.466
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.466
3h1jSMACytochrome b/0.466
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.466
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.465
1k7l544Peroxisome proliferator-activated receptor alpha/0.464
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.464
2znoS44Peroxisome proliferator-activated receptor gamma/0.464
4eajATP5'-AMP-activated protein kinase subunit gamma-1/0.464
2p83MR0Beta-secretase 13.4.23.460.463
3a4vNADNDP-sugar epimerase/0.463
3cmcNADGlyceraldehyde-3-phosphate dehydrogenase/0.463
3nx4NAPPutative oxidoreductase/0.463
4iaq2GM5-hydroxytryptamine receptor 1B/0.463
4oztP1AEcdysone receptor, putative/0.463
2dteNAIGlucose 1-dehydrogenase related protein/0.462
4qi5FADCellobiose dehydrogenase/0.462
4z34ON7Lysophosphatidic acid receptor 1/0.462
1tj0FADBifunctional protein PutA1.5.5.20.461
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.461
3sdkP3NProteasome subunit beta type-53.4.25.10.461
3sdkP3NProteasome subunit beta type-63.4.25.10.461
4j6cSTRCytochrome P450 monooxygenase/0.461
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.461
2ou2ACOHistone acetyltransferase KAT5/0.460
3b20NADGlyceraldehyde-3-phosphate dehydrogenase/0.460
3bhlTHGThymidylate synthase/0.460
3gw9VNILanosterol 14-alpha-demethylase/0.460
3sz0FADSulfide-quinone reductase/0.460
3zk5Z18Cytochrome P450 monooxygenase PikC/0.460
4j6dTESCytochrome P450 monooxygenase/0.460
4jbiNDPAlcohol dehydrogenase (Zinc)/0.460
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.459
3cylVITBasic phospholipase A2 homolog piratoxin-2/0.459
4uymVOR14-alpha sterol demethylase Cyp51B/0.459
1hdoNAPFlavin reductase (NADPH)/0.458
1yb5NAPQuinone oxidoreductase1.6.5.50.458
2ojj82AMitogen-activated protein kinase 12.7.11.240.458
2vbdV10Isopenicillin N synthase1.21.3.10.458
3deiRXBCaspase-33.4.22.560.458
4fr4STUSerine/threonine-protein kinase 32A2.7.11.10.458
2nnhREACytochrome P450 2C8/0.457
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.457
4r21STRCytochrome P450 family 17 polypeptide 2/0.457
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.457
3gkjHC3Niemann-Pick C1 protein/0.456
3wmxNADNAD dependent epimerase/dehydratase/0.456
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.456
4g3jVNTLanosterol 14-alpha-demethylase/0.456
5dr9SKEAurora kinase A2.7.11.10.456
2q61SF1Peroxisome proliferator-activated receptor gamma/0.455
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.455
3ox4NADAlcohol dehydrogenase 21.1.1.10.455
3pjuC2EDiguanylate cyclase/phosphodiesterase/0.455
4q73FADBifunctional protein PutA/0.455
5lc1NADL-threonine 3-dehydrogenase/0.455
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.454
3qlrNDPDihydrofolate reductase1.5.1.30.454
4ia3BIVVitamin D3 receptor A/0.454
1lriCLRBeta-elicitin cryptogein/0.453
1qvrANPChaperone protein ClpB/0.453
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.453
2fzmFADBifunctional protein PutA1.5.5.20.453
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.453
3efwAK8Aurora kinase A2.7.11.10.453
4q72FADBifunctional protein PutA/0.453
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
2ejvNADL-threonine 3-dehydrogenase/0.452
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.452
2oxtSAMGenome polyprotein/0.452
2pobGW4Peroxisome proliferator-activated receptor gamma/0.452
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.452
3syiFADSulfide-quinone reductase/0.452
4a6bQG8Gag-Pol polyprotein3.4.23.160.452
4aw3MYVMycinamicin IV hydroxylase/epoxidase/0.452
4iarERM5-hydroxytryptamine receptor 1B/0.452
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.452
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.452
4q71FADBifunctional protein PutA/0.452
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.451
1rdt570Peroxisome proliferator-activated receptor gamma/0.451
2bx8AZQSerum albumin/0.451
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.451
3tqhNDPQuinone oxidoreductase/0.451
3ua506XCytochrome P450 2B61.14.130.451
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.451
1fmlRTLRetinol dehydratase/0.450
1q0qNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.450
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.450
2jn3JN3Fatty acid-binding protein, liver/0.450
2npaMMBPeroxisome proliferator-activated receptor alpha/0.450
3gbuATPUncharacterized sugar kinase PH14592.7.10.450
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.450
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.450
3n7uNADFormate dehydrogenase, chloroplastic/mitochondrial/0.450
3nxuRITCytochrome P450 3A4/0.450
4frjDWBBeta-secretase 13.4.23.460.450
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.450
4pd6URINucleoside permease/0.450
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.450
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.450
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.449
2aibERGBeta-elicitin cinnamomin/0.449
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.449
2ql6ADPNicotinamide riboside kinase 1/0.449
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.449
4qe6JN3Bile acid receptor/0.449
4ruoBIVVitamin D3 receptor A/0.449
1bucFADAcyl-CoA dehydrogenase, short-chain specific1.3.8.10.448
1gypNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.448
2imkGTXAGAP009194-PA/0.448
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.448
3ijdC2FMethylenetetrahydrofolate reductase/0.448
3l0lHC3Nuclear receptor ROR-gamma/0.448
3nxxNDPDihydrofolate reductase1.5.1.30.448
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.448
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
4itfTFYVitamin D3 receptor/0.448
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.448
4kwi1TJReductase homolog/0.448
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.447
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.447
1lluNADAlcohol dehydrogenase/0.447
1xkdNAPIsocitrate dehydrogenase [NADP]/0.447
1zeoC01Peroxisome proliferator-activated receptor gamma/0.447
2c7xNRBCytochrome P450 monooxygenase PikC/0.447
2givACOHistone acetyltransferase KAT8/0.447
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.447
3p6nDSOCamphor 5-monooxygenase1.14.15.10.447
3slkNDPPolyketide synthase extender module 2/0.447
3stxBKAMethylketone synthase I/0.447
4djaFAD(6-4) photolyase/0.447
4i22IREEpidermal growth factor receptor2.7.10.10.447
5a3cNADSIR2 family protein/0.447
1fm9570Peroxisome proliferator-activated receptor gamma/0.446
1rv1IMZE3 ubiquitin-protein ligase Mdm26.3.20.446
3adaNADSubunit alpha of sarocosine oxidase/0.446
3kybFADUDP-galactopyranose mutase5.4.99.90.446
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.446
3tz3B36Acetyl-CoA carboxylase/0.446
3vrwYS5Vitamin D3 receptor/0.446
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.446
5dozNDPJamJ/0.446
1felFENRetinol-binding protein 4/0.445
1juvNDPDihydrofolate reductase1.5.1.30.445
1tj1FADBifunctional protein PutA1.5.5.20.445
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.445
2g5cNADPrephenate dehydrogenase/0.445
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.445
3bgxMEFThymidylate synthase/0.445
3dejRXCCaspase-33.4.22.560.445
4ips1G4Mycocyclosin synthase1.14.21.90.445
4l9kEHFSerum albumin/0.445
4nb6444Nuclear receptor ROR-gamma/0.445
5ab6CAANonspecific lipid-transfer protein, putative/0.445
1k74544Peroxisome proliferator-activated receptor gamma/0.444
1tj2FADBifunctional protein PutA1.5.5.20.444
2agvTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.444
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.444
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.444
2q4bNAPUncharacterized protein At5g02240/0.444
2vzmNRBCytochrome P450 monooxygenase PikC/0.444
2zb3NDPProstaglandin reductase 21.3.1.480.444
3aw9NADNAD-dependent epimerase/dehydratase/0.444
3ijoB4DGlutamate receptor 2/0.444
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.444
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.444
4ku5DCC3-oxoacyl-[ACP] synthase III/0.444
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.443
2c0iL1GTyrosine-protein kinase HCK2.7.10.20.443
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.443
3ibdCPZCytochrome P450 2B61.14.130.443
3r83Z14Cyclin-dependent kinase 22.7.11.220.443
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.443
4b722FBBeta-secretase 13.4.23.460.443
4xldBRLPeroxisome proliferator-activated receptor gamma/0.443
5dpvSKEAurora kinase A2.7.11.10.443
1a7kNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.442
1diuBDMDihydrofolate reductase1.5.1.30.442
1iyzNDPProbable quinone oxidoreductase/0.442
1mjbACOHistone acetyltransferase ESA1/0.442
1ppjANYCytochrome b/0.442
2cig1DGDihydrofolate reductase1.5.1.30.442
2e48FADD-amino-acid oxidase1.4.3.30.442
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
2iutAGSDNA translocase FtsK/0.442
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.442
2q4wFADCytokinin dehydrogenase 71.5.99.120.442
2xb5I7TTetracycline repressor protein class D/0.442
2znnS44Peroxisome proliferator-activated receptor alpha/0.442
3frqERYErythromycin resistance repressor protein/0.442
3n83ADPAldehyde dehydrogenase, mitochondrial1.2.1.30.442
3p3zP3ZPutative cytochrome P450/0.442
3u4cNDPNADPH-dependent reductase BacG/0.442
3w2cN15Aurora kinase A2.7.11.10.442
3wy0COAUncharacterized protein/0.442
4a83DXCMajor pollen allergen Bet v 1-A/0.442
4isk1JYThymidylate synthase/0.442
4j4bNAIUncharacterized protein/0.442
4j6bPLOCytochrome P450 monooxygenase/0.442
4jbtASDCytochrome P450 monooxygenase/0.442
4jx1CAHCamphor 5-monooxygenase1.14.15.10.442
4l8u9AZSerum albumin/0.442
4la0198Serum albumin/0.442
1fwkADPHomoserine kinase2.7.1.390.441
1xddAAYIntegrin alpha-L/0.441
1z7yAA5Cysteine synthase 12.5.1.470.441
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.441
2g20L1ARenin3.4.23.150.441
2jd1NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.441
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.441
3imxB84Glucokinase2.7.1.20.441
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.441
3l4sNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.441
3wxyCOAUncharacterized protein/0.441
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.441
4y8wSTRSteroid 21-hydroxylase/0.441
5k2bZMAAdenosine receptor A2a/0.441
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.440
1k6cMK1Gag-Pol polyprotein3.4.23.160.440
1rk3VDXVitamin D3 receptor/0.440
1rrmAPRLactaldehyde reductase1.1.1.770.440
1sn5T3Transthyretin/0.440
2hb7O1CVitamin D3 receptor/0.440
2po7CHDFerrochelatase, mitochondrial4.99.1.10.440
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.440
3t14FADSulfide-quinone reductase/0.440
3tqaNDPDihydrofolate reductase/0.440
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4ia2BIVVitamin D3 receptor A/0.440
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.440
5a3bAPRSIR2 family protein/0.440