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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
3eq1DPMPorphobilinogen deaminase2.5.1.61

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3eq1DPMPorphobilinogen deaminase2.5.1.611.000
3uvp048Mitogen-activated protein kinase 14/0.487
1g4tFTPThiamine-phosphate synthase/0.480
1k6tXN1Gag-Pol polyprotein3.4.23.160.480
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.475
4bc6XZNSerine/threonine-protein kinase 102.7.11.10.474
1d7yFADFerredoxin reductase/0.473
4iteTEYVitamin D3 receptor/0.473
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.473
1g67TZPThiamine-phosphate synthase/0.470
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.470
1kgjFL8Transthyretin/0.468
4be7ATPType I restriction enzyme EcoR124II R protein3.1.21.30.468
1g6cIFPThiamine-phosphate synthase/0.467
2b9wFADPutative aminooxidase/0.467
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.466
1sn0T44Transthyretin/0.465
3w0aDS5Vitamin D3 receptor/0.465
3ix9MTXDihydrofolate reductase1.5.1.30.464
4c04SFGProtein arginine N-methyltransferase 6/0.463
1g69TZPThiamine-phosphate synthase/0.462
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.461
3w0jT08Vitamin D3 receptor/0.461
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.460
1h1wATP3-phosphoinositide-dependent protein kinase 12.7.11.10.460
2bsmBSMHeat shock protein HSP 90-alpha/0.460
2q4bNAPUncharacterized protein At5g02240/0.460
1ii6ADPKinesin-like protein KIF11/0.459
1s60COAAminoglycoside N(6')-acetyltransferase type 1/0.459
1xq6NAPUncharacterized protein At5g02240/0.459
4y12AGSSerine/threonine-protein kinase PknG2.7.11.10.459
1g4sTPSThiamine-phosphate synthase/0.458
1sn5T3Transthyretin/0.458
2o4rVD5Vitamin D3 receptor/0.457
3chwATPMajor actin/0.457
4rphFADUDP-galactopyranose mutase5.4.99.90.457
1jm6ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.456
2bhiSFTCytotoxin 3/0.456
2izrBRKCasein kinase I isoform gamma-32.7.11.10.456
1osvCHCBile acid receptor/0.455
2q36ATPActin, alpha skeletal muscle/0.455
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.455
3k145352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.455
3ortAGSSerine/threonine protein kinase/0.455
4at9UTPInterleukin enhancer-binding factor 2/0.455
4l8u9AZSerum albumin/0.455
1fnnADPORC1-type DNA replication protein/0.454
1s5kCOAAminoglycoside N(6')-acetyltransferase type 1/0.454
2rioADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.454
4fhh0U3Vitamin D3 receptor A/0.454
1cm8ANPMitogen-activated protein kinase 12/0.453
1rk3VDXVitamin D3 receptor/0.453
2qocANPEphrin type-A receptor 32.7.10.10.453
4i6gFADCryptochrome-2/0.453
1nlvATPMajor actin/0.452
2hcdBIVVitamin D3 receptor A/0.452
2py3ACPFibroblast growth factor receptor 2/0.452
3w0pADPHygromycin-B 4-O-kinase2.7.1.1630.452
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
1p0hACOMycothiol acetyltransferase2.3.1.1890.451
2x7bCOAN-alpha-acetyltransferase2.3.10.451
4fyxDCPAspartate carbamoyltransferase regulatory chain/0.451
1h1vATPActin, alpha skeletal muscle/0.450
1nm1ATPMajor actin/0.450
1reoFADL-amino-acid oxidase1.4.3.20.450
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.450
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.450
2zm1KSFTyrosine-protein kinase Lck2.7.10.20.450
3d0bSNXHeat shock protein HSP 90-alpha/0.450
3s87DGTRibonucleoside-diphosphate reductase large chain 11.17.4.10.450
3sjzGNPTranslation initiation factor 2 subunit gamma/0.450
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.450
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.450
4itfTFYVitamin D3 receptor/0.450
5c8yACPTubulin tyrosine ligase/0.450
1ee0CAA2-pyrone synthase/0.449
1g6cTZPThiamine-phosphate synthase/0.449
1nmdATPMajor actin/0.449
1rjkVDZVitamin D3 receptor/0.449
1yp3ATPGlucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic2.7.7.270.449
1ywrLI9Mitogen-activated protein kinase 14/0.449
3ez2ADPPlasmid partition protein A/0.449
3pjtC2EDiguanylate cyclase/phosphodiesterase/0.449
4x2dATPFic family protein putative filamentation induced by cAMP protein/0.449
1ijjATPActin, alpha skeletal muscle/0.448
1s3zCOAAminoglycoside N(6')-acetyltransferase type 1/0.448
2yegXQGHeat shock protein HSP 90-alpha/0.448
3uwqU5POrotidine 5'-phosphate decarboxylase/0.448
3vrwYS5Vitamin D3 receptor/0.448
3zonIK1Non-receptor tyrosine-protein kinase TYK22.7.10.20.448
4a9iP9IBromodomain-containing protein 2/0.448
1h6vNDPThioredoxin reductase 1, cytoplasmic1.8.1.90.447
1hk2T44Serum albumin/0.447
1hw5CMPcAMP-activated global transcriptional regulator CRP/0.447
2bunFADAppA protein/0.447
2ev9NAPShikimate dehydrogenase (NADP(+))/0.447
2qoqANPEphrin type-A receptor 32.7.10.10.447
3ac5KZMTyrosine-protein kinase Lck2.7.10.20.447
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.447
3okxSAMS-adenosyl-L-methionine-binding protein RPA0152/0.447
3p67FMNPentaerythritol tetranitrate reductase/0.447
3w5tLHPVitamin D3 receptor/0.447
4p13FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.447
4rd2GNPTranslation initiation factor 2 subunit gamma/0.447
4y0xADPSerine/threonine-protein kinase PknG2.7.11.10.447
1fndA2PFerredoxin--NADP reductase, chloroplastic1.18.1.20.446
1g1lDAUGlucose-1-phosphate thymidylyltransferase/0.446
1k6cMK1Gag-Pol polyprotein3.4.23.160.446
1o6yACPSerine/threonine-protein kinase PknB2.7.11.10.446
1txiTX5Vitamin D3 receptor/0.446
1zyjBI5Mitogen-activated protein kinase 14/0.446
2itpAEEEpidermal growth factor receptor2.7.10.10.446
2q5qTPWIndole-3-pyruvate decarboxylase4.1.1.740.446
3a783EVVitamin D3 receptor/0.446
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.446
3vjoANPEpidermal growth factor receptor2.7.10.10.446
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4ct1ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.446
4qms1N1Serine/threonine-protein kinase 242.7.11.10.446
1aj8COACitrate synthase/0.445
2b1pAIZMitogen-activated protein kinase 102.7.11.240.445
2dq7STUTyrosine-protein kinase Fyn2.7.10.20.445
2hamC33Vitamin D3 receptor/0.445
2hb7O1CVitamin D3 receptor/0.445
2itqITQEpidermal growth factor receptor2.7.10.10.445
3pcrGTPADP-ribosylation factor 6/0.445
4ho8UPGGlucose-1-phosphate thymidylyltransferase/0.445
4lj8ADPChaperone protein ClpB/0.445
4nt03DUOrotidine 5'-phosphate decarboxylase4.1.1.230.445
4wkqIREEpidermal growth factor receptor2.7.10.10.445
1h5rTHMGlucose-1-phosphate thymidylyltransferase 1/0.444
1qz5ATPActin, alpha skeletal muscle/0.444
2d0oADPDiol dehydratase-reactivating factor alpha subunit/0.444
2ivuZD6Proto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.444
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.444
3f8kCOAUncharacterized protein/0.444
3jvhHHV2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.444
4egkRDCHeat shock protein HSP 90-alpha/0.444
4g210VPVitamin D3 receptor A/0.444
4riyADPEpidermal growth factor receptor2.7.10.10.444
5c88COAN-alpha-acetyltransferase/0.444
1ie8KH1Vitamin D3 receptor/0.443
1jbpADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
1njfAGSDNA polymerase III subunit tau2.7.7.70.443
1svmATPLarge T antigen3.6.40.443
1y56FMNUncharacterized protein/0.443
1y56FMN382aa long hypothetical sarcosine oxidase/0.443
2b56UTPRNA editing complex protein MP57/0.443
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.443
2itnANPEpidermal growth factor receptor2.7.10.10.443
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.443
2xkaGSPCell division protein FtsZ/0.443
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.443
3tdl11DSerum albumin/0.443
3tqhNDPQuinone oxidoreductase/0.443
3ttjJBIMitogen-activated protein kinase 102.7.11.240.443
4c4g7RODual specificity protein kinase TTK2.7.12.10.443
4e2bFMNDehydrogenase/0.443
4enyJ19Serine/threonine-protein kinase pim-12.7.11.10.443
4iebANPCalmodulin-domain protein kinase 1/0.443
4jrvKJVEpidermal growth factor receptor2.7.10.10.443
5awmANPStress-activated protein kinase JNK2.7.11.240.443
1ju6LYAThymidylate synthase2.1.1.450.442
1m17AQ4Epidermal growth factor receptor2.7.10.10.442
1ykdCMPAdenylate cyclase/0.442
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.442
2qhm7CSSerine/threonine-protein kinase Chk12.7.11.10.442
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.442
3upf0BUPolyprotein/0.442
3w0iO11Vitamin D3 receptor/0.442
4s32ANPMitogen-activated protein kinase 12.7.11.240.442
5iua6DXAdenosine receptor A2a/0.442
1mruAGSSerine/threonine-protein kinase PknB2.7.11.10.441
1rkgVD1Vitamin D3 receptor/0.441
1vruAAPGag-Pol polyprotein2.7.7.490.441
2o4jVD4Vitamin D3 receptor/0.441
2xpvMIYTetracycline repressor protein class D/0.441
3mdmFJZCholesterol 24-hydroxylase/0.441
3mnrSD1Heat shock protein HSP 90-alpha/0.441
3oibFDAPutative acyl-CoA dehydrogenase/0.441
3qaqQAQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4kxl6C62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.441
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.441
4mxoDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.441
4xgxADPFAD:protein FMN transferase/0.441
5amnDTQProto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.441
1a9xADPCarbamoyl-phosphate synthase large chain/0.440
1g3lTRHGlucose-1-phosphate thymidylyltransferase/0.440
1r9oFLPCytochrome P450 2C9/0.440
1vyrFMNPentaerythritol tetranitrate reductase/0.440
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2a4zBYMPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
2yee2ECHeat shock protein HSP 90-alpha/0.440
3a8tATPAdenylate isopentenyltransferase/0.440
3icsCOACoenzyme A disulfide reductase/0.440
3q5iANPProtein kinase, putative/0.440
4dfl0K0Tyrosine-protein kinase SYK2.7.10.20.440
4i8qNADPutative betaine aldehyde dehyrogenase/0.440