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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
4mxaBK7Calmodulin-like domain protein kinase isoenzyme gamma, related

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4mxaBK7Calmodulin-like domain protein kinase isoenzyme gamma, related/1.000
3vrzVRZTyrosine-protein kinase HCK2.7.10.20.548
2c0tL3GTyrosine-protein kinase HCK2.7.10.20.530
2c0iL1GTyrosine-protein kinase HCK2.7.10.20.521
3vs4VSFTyrosine-protein kinase HCK2.7.10.20.512
3h0aD30Peroxisome proliferator-activated receptor gamma/0.505
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.504
4lgh0JNProto-oncogene tyrosine-protein kinase Src2.7.10.20.497
4fic0ULProto-oncogene tyrosine-protein kinase Src2.7.10.20.489
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.488
3w2cN15Aurora kinase A2.7.11.10.487
5kjePFBAlcohol dehydrogenase E chain1.1.1.10.487
3vid4TTVascular endothelial growth factor receptor 22.7.10.10.483
4uyaAGSMitogen-activated protein kinase kinase kinase 212.7.11.250.481
5kjcPFBAlcohol dehydrogenase E chain1.1.1.10.481
3qlfPD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.480
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.480
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.478
3tvuB37Acetyl-CoA carboxylase/0.478
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.476
4dggI76Proto-oncogene tyrosine-protein kinase Src2.7.10.20.476
5kj1PFBAlcohol dehydrogenase E chain1.1.1.10.476
2ca0PXICytochrome P450 monooxygenase PikC/0.475
1hzzNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.473
2uznC96Cyclin-dependent kinase 22.7.11.220.473
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.472
3p6pA6BCamphor 5-monooxygenase1.14.15.10.472
3le62BZCyclin-dependent kinase 22.7.11.220.471
5kcpPFBAlcohol dehydrogenase E chain1.1.1.10.470
3t2zFADSulfide-quinone reductase/0.469
4jayFADUDP-N-acetylenolpyruvoylglucosamine reductase/0.469
4nfhPFBAlcohol dehydrogenase E chain1.1.1.10.469
3abaFLICytochrome P450/0.468
3ffi3OBGag-Pol polyprotein2.7.7.490.468
3ictCOACoenzyme A disulfide reductase/0.468
1ot7CHCBile acid receptor/0.467
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.467
3icsCOACoenzyme A disulfide reductase/0.467
3p6oETGCamphor 5-monooxygenase1.14.15.10.467
3oq6PFBAlcohol dehydrogenase E chain1.1.1.10.466
4hee14RPeroxisome proliferator-activated receptor gamma/0.466
3cs8BRLPeroxisome proliferator-activated receptor gamma/0.465
3nbpJGZGag-Pol polyprotein2.7.7.490.465
3zk5Z18Cytochrome P450 monooxygenase PikC/0.465
4ryvZEAProtein LlR18A/0.465
5cdtPFBAlcohol dehydrogenase E chain1.1.1.10.465
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.464
3igoANPCalmodulin-domain protein kinase 1, putative/0.464
4b7sQLECytochrome P450 monooxygenase PikC/0.464
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.464
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.464
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.463
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.463
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.463
1ie4T44Transthyretin/0.462
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.462
2c7xNRBCytochrome P450 monooxygenase PikC/0.461
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.461
4i3vNADAldehyde dehydrogenase (NAD+)/0.461
1heuNADAlcohol dehydrogenase E chain1.1.1.10.460
2po7CHDFerrochelatase, mitochondrial4.99.1.10.460
3l8p0CEAngiopoietin-1 receptor2.7.10.10.460
5a3bAPRSIR2 family protein/0.460
2q61SF1Peroxisome proliferator-activated receptor gamma/0.459
4kaoKAOFocal adhesion kinase 12.7.10.20.459
1y4lSVRBasic phospholipase A2 homolog 2/0.458
1yb5NAPQuinone oxidoreductase1.6.5.50.458
3p6mDSOCamphor 5-monooxygenase1.14.15.10.458
3vnt0JAVascular endothelial growth factor receptor 22.7.10.10.458
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.458
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.457
2bi4NADLactaldehyde reductase1.1.1.770.457
2fzwNADAlcohol dehydrogenase class-31.1.1.10.457
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.457
5bsfNADPyrroline-5-carboxylate reductase/0.457
1diuBDMDihydrofolate reductase1.5.1.30.456
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.456
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.456
2y00Y01Beta-1 adrenergic receptor/0.455
3w33W19Epidermal growth factor receptor2.7.10.10.455
4xyeNADFormate dehydrogenase/0.455
5kj6PFBAlcohol dehydrogenase E chain1.1.1.10.455
1lsoNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.454
2p4yC03Peroxisome proliferator-activated receptor gamma/0.454
3b8q900Vascular endothelial growth factor receptor 22.7.10.10.454
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.454
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.454
4l4xNDPAmphI/0.454
1jpaANPEphrin type-B receptor 22.7.10.10.453
1ml3NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.453
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.453
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.453
3deiRXBCaspase-33.4.22.560.453
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.453
4dwvPFBAlcohol dehydrogenase E chain1.1.1.10.453
4i2q1BTGag-Pol polyprotein2.7.7.490.453
4kl9NDPDihydrofolate reductase1.5.1.30.453
4xldBRLPeroxisome proliferator-activated receptor gamma/0.453
2q5p241Peroxisome proliferator-activated receptor gamma/0.452
2c6hPXICytochrome P450 monooxygenase PikC/0.451
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.451
3h0sB38Acetyl-CoA carboxylase/0.451
4l2iFADElectron transfer flavoprotein alpha/beta-subunit/0.451
4yuqKS1Calmodulin-like domain protein kinase/0.451
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.450
1k6cMK1Gag-Pol polyprotein3.4.23.160.450
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.450
3b70NAPEnoyl reductase LovC10.450
3fl8RARDihydrofolate reductase/0.450
3ormAGSSerine/threonine protein kinase/0.450
3p6nDSOCamphor 5-monooxygenase1.14.15.10.450
3v04V04Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.450
1ml6GBXGlutathione S-transferase A22.5.1.180.449
1re9DSOCamphor 5-monooxygenase1.14.15.10.449
2om9AJAPeroxisome proliferator-activated receptor gamma/0.449
4ng5PFBAlcohol dehydrogenase E chain1.1.1.10.449
4zseANPEpidermal growth factor receptor2.7.10.10.449
1jvsNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.448
1me8RVPInosine-5'-monophosphate dehydrogenase/0.448
2ft9CHDFatty acid-binding protein 2, liver/0.448
3gubGUBDeath-associated protein kinase 12.7.11.10.448
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.448
3zuyTCHTransporter/0.448
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.448
1osvCHCBile acid receptor/0.447
2hsdNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.447
2i5bADPPyridoxine kinase/0.447
2zbzVDXVitamin D3 dihydroxylase/0.447
3vspEK8Peroxisome proliferator-activated receptor gamma/0.447
4otwDB8Receptor tyrosine-protein kinase erbB-32.7.10.10.447
4r20AERCytochrome P450 family 17 polypeptide 2/0.447
4tuvCPZCytochrome P450 1191.140.447
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.446
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
2w0jZATSerine/threonine-protein kinase Chk22.7.11.10.446
3a60STURibosomal protein S6 kinase beta-12.7.11.10.446
4c8b0LIReceptor-interacting serine/threonine-protein kinase 22.7.11.10.446
4z9rNADOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.446
5cdgPFBAlcohol dehydrogenase E chain1.1.1.10.446
1lluNADAlcohol dehydrogenase/0.445
3p7nFMNLight-activated DNA-binding protein EL222/0.445
4aoxFADSteroid monooxygenase/0.445
4isk1JYThymidylate synthase/0.445
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.445
4yzcSTUSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.445
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.444
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
2ftoCB3Thymidylate synthase/0.444
2jd1NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.444
2vzmNRBCytochrome P450 monooxygenase PikC/0.444
3gu7ADPDeath-associated protein kinase 12.7.11.10.444
3h1jSMACytochrome b/0.444
3icrCOACoenzyme A disulfide reductase/0.444
3kljFADNADH-rubredoxin oxidoreductase1.18.1.10.444
3tmz06XCytochrome P450 2B41.14.14.10.444
3v5l0G1Tyrosine-protein kinase ITK/TSK2.7.10.20.444
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
4elb34RDihydrofolate reductase/0.444
4japCOAAlpha-pyrone synthesis polyketide synthase-like Pks112.3.10.444
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.444
1i6xCMPcAMP-activated global transcriptional regulator CRP/0.443
2bx8AZQSerum albumin/0.443
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.443
3pghFLPProstaglandin G/H synthase 21.14.99.10.443
4xumIMNPeroxisome proliferator-activated receptor gamma/0.443
5cmsAPRO-acetyl-ADP-ribose deacetylase/0.443
1hetNADAlcohol dehydrogenase E chain1.1.1.10.442
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.442
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.442
2gejGDDPhosphatidyl-myo-inositol mannosyltransferase2.4.1.570.442
2gs7ANPEpidermal growth factor receptor2.7.10.10.442
2y05NAPProstaglandin reductase 1/0.442
2ykbYKBHeat shock protein HSP 90-alpha/0.442
2zb3NDPProstaglandin reductase 21.3.1.480.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3iaeD7KBenzaldehyde lyase/0.442
3qrwNDPPutative ketoacyl reductase1.3.10.442
4eevL1XHepatocyte growth factor receptor2.7.10.10.442
4fehFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.442
4g48PZBMycocyclosin synthase1.14.21.90.442
4ma628EAra h 8 allergen/0.442
4q71FADBifunctional protein PutA/0.442
4wjiNAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase/0.442
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.441
1oiqHDUCyclin-dependent kinase 22.7.11.220.441
1uyfPU1Heat shock protein HSP 90-alpha/0.441
2c6eHPMAurora kinase A2.7.11.10.441
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3hng8STVascular endothelial growth factor receptor 12.7.10.10.441
3m8qDJZGag-Pol polyprotein2.7.7.490.441
3sgx0FWDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.441
3zuxTCHTransporter/0.441
4i0bCMPcAMP-activated global transcriptional regulator CRP/0.441
4pd6URINucleoside permease/0.441
4qe6JN3Bile acid receptor/0.441
4xd2NAIAlcohol dehydrogenase E chain1.1.1.10.441
4xiwAZMCarbonic anhydrase, alpha type/0.441
5av2KMPDeath-associated protein kinase 12.7.11.10.441
5cdsNAJAlcohol dehydrogenase E chain1.1.1.10.441
1llqNADNAD-dependent malic enzyme, mitochondrial1.1.1.380.440
2p33J07Mitogen-activated protein kinase 102.7.11.240.440
2xk9XK9Serine/threonine-protein kinase Chk22.7.11.10.440
2ycrHCWSerine/threonine-protein kinase Chk22.7.11.10.440
3d8xFADThioredoxin reductase 11.8.1.90.440
3nwyGTPUridylate kinase/0.440
3pgqGY3Acetyl-CoA carboxylase/0.440
3r9dX6BCyclin-dependent kinase 22.7.11.220.440
3uhl2NCGag-Pol polyprotein3.4.23.160.440
3w18N13Aurora kinase A2.7.11.10.440
3wi6YRZMAP kinase-activated protein kinase 22.7.11.10.440
4b7dQLECytochrome P450 monooxygenase PikC/0.440
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
4ubsDIFPentalenic acid synthase1.14.15.110.440