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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
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/1.000
4ax8ADPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.545
1zeoC01Peroxisome proliferator-activated receptor gamma/0.488
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.487
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.487
3l0lHC3Nuclear receptor ROR-gamma/0.483
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.483
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.481
1cqp803Integrin alpha-L/0.480
3hyoADPPyridoxal kinase/0.478
5cvhADPCasein kinase II subunit alpha2.7.11.10.477
2jizANPATP synthase subunit beta, mitochondrial3.6.3.140.476
2cdaNAPGlucose 1-dehydrogenase/0.474
5bt42LOBromodomain-containing protein 4/0.474
1r2jFADFkbI/0.473
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.471
3vt7VDXVitamin D3 receptor/0.471
4ocvANPAminoglycoside phosphotransferase/0.470
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.469
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.468
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.467
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.466
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.466
2zevB71Geranylgeranyl pyrophosphate synthase/0.465
4mwhATPCasein kinase II subunit alpha2.7.11.10.465
1rfuADPPyridoxal kinase2.7.1.350.464
3q43D66M1 family aminopeptidase3.4.110.464
4lfiGNPCasein kinase II subunit alpha2.7.11.10.463
4ryvZEAProtein LlR18A/0.463
2w6mOA1Biotin carboxylase6.3.4.140.462
2w6qOA5Biotin carboxylase6.3.4.140.462
4fi1ATPCasein kinase II subunit alpha2.7.11.10.462
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.461
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.461
3vt9YI4Vitamin D3 receptor/0.461
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.461
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
4ix6ADPUncharacterized protein/0.461
4jlj1NMDeoxycytidine kinase2.7.1.740.460
1xddAAYIntegrin alpha-L/0.459
2e0nSAHPrecorrin-2 C20-methyltransferase/0.459
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.459
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.459
4l8u9AZSerum albumin/0.458
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.457
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.456
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.456
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.456
2izrBRKCasein kinase I isoform gamma-32.7.11.10.455
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.455
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3tk3CPZCytochrome P450 2B41.14.14.10.455
3gw9VNILanosterol 14-alpha-demethylase/0.453
3sayOFTGlycogen synthase kinase-3 beta2.7.11.260.453
3vt8YI3Vitamin D3 receptor/0.453
3zxzKRWHepatocyte growth factor receptor2.7.10.10.453
5irnADPNucleotide binding oligomerization domain containing 2/0.453
1pkfEPDEpothilone C/D epoxidase1.140.452
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.452
3ibqATPPyridoxal kinase/0.452
1s7gNADNAD-dependent protein deacylase 2/0.451
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.451
3ambVX6cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.451
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.451
1bwsNDPGDP-L-fucose synthase/0.450
1bygSTUTyrosine-protein kinase CSK/0.450
1hb1OCVIsopenicillin N synthase1.21.3.10.450
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.450
2rabNADGlutathione amide reductase/0.450
3hl7I46Mitogen-activated protein kinase 14/0.450
3pqbVGPPutative oxidoreductase/0.450
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.450
3v94WYQPhosphodiesterase/0.450
4iwv1J9Glucokinase2.7.1.20.450
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1opbRETRetinol-binding protein 2/0.449
1zg32HIIsoflavone 4'-O-methyltransferase/0.449
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.449
2w71L23Biotin carboxylase6.3.4.140.449
3pe2E1BCasein kinase II subunit alpha2.7.11.10.449
4i8vBHFCytochrome P450 1A11.14.14.10.449
4iq71G9Mycocyclosin synthase1.14.21.90.449
4jqeANPCasein kinase II subunit alpha2.7.11.10.449
4mgiCMPRap guanine nucleotide exchange factor 4/0.449
1s5kCOAAminoglycoside N(6')-acetyltransferase type 1/0.448
1umlFR4Adenosine deaminase3.5.4.40.448
2dvlFADAcyl-CoA dehydrogenase/0.448
3jziJZLBiotin carboxylase6.3.4.140.448
3oriAGSSerine/threonine protein kinase/0.448
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4en4ATPPyridoxal kinase2.7.1.350.448
4nh82LCHeat shock protein HSP 90-alpha/0.448
4r7uUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.448
4r8qADPMitotic checkpoint serine/threonine-protein kinase BUB12.7.11.10.448
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.447
1jtqLY3Thymidylate synthase/0.447
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.447
2lbaCHOFatty acid binding protein 6/0.447
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2p33J07Mitogen-activated protein kinase 102.7.11.240.447
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.447
2uxoTACHTH-type transcriptional regulator TtgR/0.447
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.447
4n702HXSerine/threonine-protein kinase pim-12.7.11.10.447
1kqwRTLCellular retinol-binding protein type II/0.446
1kzjCB3Thymidylate synthase/0.446
1ndzFR5Adenosine deaminase3.5.4.40.446
1vbnYSATyrosine--tRNA ligase6.1.1.10.446
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
2ij7TPFMycocyclosin synthase1.14.21.90.446
3c3xNAPEugenol synthase 11.1.1.3180.446
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.446
4dliIRGMitogen-activated protein kinase 14/0.446
4do30LAFatty-acid amide hydrolase 13.5.1.990.446
4ips1G4Mycocyclosin synthase1.14.21.90.446
4qmySTUSerine/threonine-protein kinase 242.7.11.10.446
4y8wSTRSteroid 21-hydroxylase/0.446
1v79FR7Adenosine deaminase3.5.4.40.445
2eufLQQCyclin-dependent kinase 62.7.11.220.445
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.445
2puiADPMethylthioribose kinase2.7.1.1000.445
2yisI46Mitogen-activated protein kinase 14/0.445
2z7gEH9Adenosine deaminase3.5.4.40.445
3rvhHQ2Lysine-specific demethylase 4A1.14.110.445
4py6R78Bromodomain protein, putative/0.445
3uzcT4EAdenosine receptor A2a/0.445
1m13HYFNuclear receptor subfamily 1 group I member 2/0.444
1ppjANYCytochrome b/0.444
1u4dDBQActivated CDC42 kinase 1/0.444
1vbmYSATyrosine--tRNA ligase6.1.1.10.444
2pauD5M5'-deoxynucleotidase YfbR/0.444
2x9dITCTetracycline repressor protein class D/0.444
3amaSKEcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
4e4m0NHTyrosine-protein kinase JAK2/0.444
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.444
1rfvADPPyridoxal kinase2.7.1.350.443
2po7CHDFerrochelatase, mitochondrial4.99.1.10.443
2vn1FK5Peptidylprolyl isomerase/0.443
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
1iyzNDPProbable quinone oxidoreductase/0.442
1j49NADD-lactate dehydrogenase1.1.1.280.442
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.442
2vnkFADNADPH:ferredoxin reductase/0.442
3fkoFKOMitogen-activated protein kinase 14/0.442
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.442
4g3jVNTLanosterol 14-alpha-demethylase/0.442
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1s60COAAminoglycoside N(6')-acetyltransferase type 1/0.441
2v59LZKBiotin carboxylase6.3.4.140.441
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3h3qH13Collagen type IV alpha-3-binding protein/0.441
3jzdNADMaleylacetate reductase/0.441
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.441
1k7fIAVTryptophan synthase alpha chain/0.440
1lb9DNQGlutamate receptor 2/0.440
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.440
2jfz003Glutamate racemase/0.440
2q28ADPOxalyl-CoA decarboxylase4.1.1.80.440
2xy93ESAngiotensin-converting enzyme3.2.10.440
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.440
2yxuATPPyridoxal kinase2.7.1.350.440
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.440
3mdmFJZCholesterol 24-hydroxylase/0.440
3p3zP3ZPutative cytochrome P450/0.440
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.440
4cztCPSCBL-interacting serine/threonine-protein kinase 232.7.11.10.440
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.440