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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
1av5AP2Histidine triad nucleotide-binding protein 13

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1av5AP2Histidine triad nucleotide-binding protein 131.000
1rzy5ASHistidine triad nucleotide-binding protein 130.614
4eqgA5AHistidine triad nucleotide-binding protein 130.568
5i2fBS5Histidine triad nucleotide-binding protein 130.567
3oxk5GPHistidine triad nucleotide-binding protein30.557
3qgzADNHistidine triad nucleotide-binding protein 130.552
4eqeKAAHistidine triad nucleotide-binding protein 130.538
5fitAP2Bis(5'-adenosyl)-triphosphatase3.6.1.290.516
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.505
3l0lHC3Nuclear receptor ROR-gamma/0.496
3n1s5GPPurine nucleoside phosphoramidase/0.496
2z3uCRRCytochrome P450/0.494
3gkjHC3Niemann-Pick C1 protein/0.494
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.492
1o6rR19Squalene--hopene cyclase4.2.1.1290.489
3n1t5GPPurine nucleoside phosphoramidase/0.489
3tdaPN0Cytochrome P450 2D6/0.488
2iviACWIsopenicillin N synthase1.21.3.10.487
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.486
1nhkCMPNucleoside diphosphate kinase2.7.4.60.485
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.484
1kyzFERCaffeic acid 3-O-methyltransferase2.1.1.680.483
3zeiAWHO-acetylserine sulfhydrylase/0.483
3a1l2CCCytochrome P450/0.482
3cid318Beta-secretase 13.4.23.460.481
1rf7DHFDihydrofolate reductase1.5.1.30.479
3acy702Dehydrosqualene synthase/0.479
3cic316Beta-secretase 13.4.23.460.479
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.478
4ej1FOLDihydrofolate reductase1.5.1.30.478
2vbpVB1Isopenicillin N synthase1.21.3.10.477
4egu5GPPutative histidine triad (HIT) protein/0.477
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.477
2iqgF2IBeta-secretase 13.4.23.460.476
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.476
4c49HCYCorticosteroid-binding globulin/0.475
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.473
3cib314Beta-secretase 13.4.23.460.473
3hf6LX0Tryptophan 5-hydroxylase 11.14.16.40.473
1ygkRRCPyridoxal kinase2.7.1.350.472
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.472
3lpkZ76Beta-secretase 13.4.23.460.472
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.472
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.471
2p83MR0Beta-secretase 13.4.23.460.470
3zkyWT4Isopenicillin N synthase1.21.3.10.470
4iaq2GM5-hydroxytryptamine receptor 1B/0.470
2gd0MRSProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.469
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.469
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.468
3ixj586Beta-secretase 13.4.23.460.468
4bb3KKAIsopenicillin N synthase1.21.3.10.468
4h5cYS4Farnesyl pyrophosphate synthase2.5.1.100.468
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.467
2vbdV10Isopenicillin N synthase1.21.3.10.467
3lpiZ74Beta-secretase 13.4.23.460.467
3uwlFOZThymidylate synthase/0.467
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.467
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.466
3q43D66M1 family aminopeptidase3.4.110.466
4nt3ZAWLactoperoxidase1.11.1.70.466
1fmlRTLRetinol dehydratase/0.465
1h36R88Squalene--hopene cyclase4.2.1.1290.465
3vf2ADPnebramycin 5' synthase6.1.2.20.465
4fizCUE17beta-hydroxysteroid dehydrogenase/0.465
4rv9SAHD-mycarose 3-C-methyltransferase/0.465
1hb1OCVIsopenicillin N synthase1.21.3.10.464
2idkC2FGlycine N-methyltransferase2.1.1.200.464
2y6fM9FIsopenicillin N synthase1.21.3.10.464
3hf8ML0Tryptophan 5-hydroxylase 11.14.16.40.464
3ou7SAMSAM-dependent methyltransferase/0.464
1fwkADPHomoserine kinase2.7.1.390.463
3dm6757Beta-secretase 13.4.23.460.463
3e2sFADBifunctional protein PutA1.5.5.20.463
1hb3SCVIsopenicillin N synthase1.21.3.10.462
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
3f3y4OABile salt sulfotransferase2.8.2.140.462
4phlPILPhosphodiesterase/0.462
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.461
1icqOPD12-oxophytodienoate reductase 11.3.1.420.461
1jomFFODihydrofolate reductase1.5.1.30.461
3gkiCLRNiemann-Pick C1 protein/0.461
3hazFADBifunctional protein PutA/0.461
3hywDCQSulfide-quinone reductase/0.461
3kytHC2Nuclear receptor ROR-gamma/0.461
3ohh3HHBeta-secretase 13.4.23.460.461
4h5eYS4Farnesyl pyrophosphate synthase2.5.1.100.461
1bk0ACVIsopenicillin N synthase1.21.3.10.460
1khrCOAStreptogramin A acetyltransferase2.3.10.460
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.460
2o7pNAPRiboflavin biosynthesis protein RibD/0.460
4o8aFADBifunctional protein PutA1.2.1.880.460
2ycyP32Beta-1 adrenergic receptor/0.460
1nbhSAMGlycine N-methyltransferase2.1.1.200.459
1qjfACSIsopenicillin N synthase1.21.3.10.459
3q9bB3NAcetylpolyamine amidohydrolase/0.459
3zkuHCVIsopenicillin N synthase1.21.3.10.459
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.458
2lfoGCHFatty acid-binding protein, liver/0.458
3n19FNRXenobiotic reductase/0.458
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.458
2e0nSAHPrecorrin-2 C20-methyltransferase/0.457
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.457
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.457
4qi9MTXDihydrofolate reductase/0.457
5hi6MTXDihydrofolate reductase/0.457
1iyzNDPProbable quinone oxidoreductase/0.456
1oc1ASVIsopenicillin N synthase1.21.3.10.456
1ppjANYCytochrome b/0.456
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.456
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.456
1yhjR6CPyridoxal kinase2.7.1.350.456
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.456
3k5gBJCBeta-secretase 13.4.23.460.456
3zm5IGMUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.456
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.456
4g95OAGDihydrofolate reductase1.5.1.30.456
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.455
1lf3EH5Plasmepsin-23.4.23.390.455
1pz1NAPGeneral stress protein 69/0.455
1rc4DDFDihydrofolate reductase1.5.1.30.455
1zw9H64ATP-dependent molecular chaperone HSP82/0.455
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.455
3zsh469Mitogen-activated protein kinase 14/0.455
4at0FADPossible succinate dehydrogenase/0.455
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.455
1s0xC3SNuclear receptor ROR-alpha/0.454
1ygjRMCPyridoxal kinase2.7.1.350.454
2d0kFOLDihydrofolate reductase1.5.1.30.454
3qm4PN0Cytochrome P450 2D6/0.454
4j6bPLOCytochrome P450 monooxygenase/0.454
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
2d29FADAcyl-CoA dehydrogenase/0.453
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.453
3hziATPSerine/threonine-protein kinase toxin HipA/0.453
3oafOAGDihydrofolate reductase1.5.1.30.453
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.453
4ea2RWZDehydrosqualene synthase/0.453
4elb34RDihydrofolate reductase/0.453
4ez8DHFThymidylate synthase2.1.1.450.453
5k2cZMAAdenosine receptor A2a/0.453
1m13HYFNuclear receptor subfamily 1 group I member 2/0.452
1nbiSAMGlycine N-methyltransferase2.1.1.200.452
3ujlA8SAbscisic acid receptor PYL2/0.452
3w0uHPWLactoylglutathione lyase4.4.1.50.452
4ifvT27Gag-Pol polyprotein2.7.7.490.452
4q73FADBifunctional protein PutA/0.452
4ryvZEAProtein LlR18A/0.452
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.451
1qiqACCIsopenicillin N synthase1.21.3.10.451
2a4xBLMMitomycin-binding protein/0.451
2fzhDH1Dihydrofolate reductase1.5.1.30.451
3pg3DG7Mitogen-activated protein kinase 14/0.451
3qls55VDihydrofolate reductase1.5.1.30.451
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4if5ACOAlpha-tubulin N-acetyltransferase 1/0.451
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.451
4ydqHFGProline--tRNA ligase6.1.1.150.451
1mgoNADAlcohol dehydrogenase E chain1.1.1.10.450
1re7FOLDihydrofolate reductase1.5.1.30.450
1uyePU9Heat shock protein HSP 90-alpha/0.450
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.450
3u8dU8DPhospholipase A2, membrane associated/0.450
3vewADPnebramycin 5' synthase6.1.2.20.450
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.450
1diuBDMDihydrofolate reductase1.5.1.30.449
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.449
2iyaZIOOleandomycin glycosyltransferase/0.449
2yimMC4Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.449
3bl7DD1m7GpppX diphosphatase3.6.1.590.449
3v0o4GWHisto-blood group ABO system transferase/0.449
4h3g10QBeta-secretase 13.4.23.460.449
4kf1HT5Aryldialkylphosphatase3.1.8.10.449
5ab7MLCNonspecific lipid-transfer protein, putative/0.449
5k2aZMAAdenosine receptor A2a/0.449
1tj2FADBifunctional protein PutA1.5.5.20.448
2gciMRRProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.448
2y1w849Histone-arginine methyltransferase CARM1/0.448
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.448
3upyFOMOxidoreductase, putative/0.448
3w0c6DSVitamin D3 receptor/0.448
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.448
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.448
4deg0JJHepatocyte growth factor receptor2.7.10.10.448
4lc71WPBeta-secretase 13.4.23.460.448
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.448
1i9c5ADGlutamate mutase epsilon subunit/0.447
1u1d181Uridine phosphorylase2.4.2.30.447
1ychFMNNitric oxide reductase10.447
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.447
3kmyD8YBeta-secretase 13.4.23.460.447
3tgyASCLactoperoxidase1.11.1.70.447
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.447
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4frkDWDBeta-secretase 13.4.23.460.447
4ia3BIVVitamin D3 receptor A/0.447
5c41ACPRibokinase/0.447
1f4gTP4Thymidylate synthase/0.446
1rd7FOLDihydrofolate reductase1.5.1.30.446
1uzwCDHIsopenicillin N synthase1.21.3.10.446
1z7yAA5Cysteine synthase 12.5.1.470.446
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.446
2g94ZPQBeta-secretase 13.4.23.460.446
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2qk8MTXDihydrofolate reductase/0.446
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.446
3o9lLPNRenin3.4.23.150.446
3skgPB8Beta-secretase 13.4.23.460.446
4bj9UHBTankyrase-22.4.2.300.446
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.446
4lb2DM5Serum albumin/0.446
4onqSFGDNA methyltransferase/0.446
4qmpDKISerine/threonine-protein kinase 242.7.11.10.446
4x5iFOLDihydrofolate reductase1.5.1.30.446
4xe606UDihydrofolate reductase1.5.1.30.446
5k2dZMAAdenosine receptor A2a/0.446
1blzACVIsopenicillin N synthase1.21.3.10.445
1exa394Retinoic acid receptor gamma/0.445
1fcy564Retinoic acid receptor gamma/0.445
1kk4ACOStreptogramin A acetyltransferase2.3.10.445
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.445
1xmmM7Gm7GpppX diphosphatase3.6.1.590.445
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.445
3deiRXBCaspase-33.4.22.560.445
3up0D7SaceDAF-12/0.445
3v94WYQPhosphodiesterase/0.445
3w0nANPHygromycin-B 4-O-kinase2.7.1.1630.445
4b4w9L9Bifunctional protein FolD/0.445
4dpi0N1Beta-secretase 13.4.23.460.445
4ekl0RFRAC-alpha serine/threonine-protein kinase2.7.11.10.445
4nieNBHNuclear receptor ROR-gamma/0.445
5a2yUTPMitochondrial poly(A) polymerase/0.445
5f2kSAHUncharacterized protein/0.445
5kf9ACOPredicted acetyltransferase/0.445
5uviZMAAdenosine receptor A2a/0.445
3ny8JRZBeta-2 adrenergic receptor/0.445
1eqbFFOSerine hydroxymethyltransferase2.1.2.10.444
1fcx184Retinoic acid receptor gamma/0.444
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.444
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3thrC2FGlycine N-methyltransferase2.1.1.200.444
3up3XCAaceDAF-12/0.444
3vtdTKDVitamin D3 receptor/0.444
4elf35IDihydrofolate reductase/0.444
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4h9506UDihydrofolate reductase1.5.1.30.444
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4jlk1NODeoxycytidine kinase2.7.1.740.444
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.444
5ab6CAANonspecific lipid-transfer protein, putative/0.444
5g53NECAdenosine receptor A2a/0.444
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.443
1nvtNAPShikimate dehydrogenase (NADP(+))/0.443
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2aclL05Oxysterols receptor LXR-alpha/0.443
2dxdANPNucleoside diphosphate kinase2.7.4.60.443
3fl8RARDihydrofolate reductase/0.443
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.443
3ou2SAHSAM-dependent methyltransferase/0.443
3vt65YIVitamin D3 receptor/0.443
4ea13RXDehydrosqualene synthase/0.443
4f6xZYLDehydrosqualene synthase/0.443
4knzCB3Thymidylate synthase/0.443
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
4rvgTYDD-mycarose 3-C-methyltransferase/0.443
4ys0ADPProtein translocase subunit SecA/0.443
5cvfATPCasein kinase II subunit alpha2.7.11.10.443
1b87ACOAac(6')-Ii protein/0.442
1c3eGARPhosphoribosylglycinamide formyltransferase/0.442
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
1w06W05Isopenicillin N synthase1.21.3.10.442
2b378PSEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2oa1FADFlavin-dependent tryptophan halogenase RebH1.14.19.90.442
2vkmBSDBeta-secretase 13.4.23.460.442
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.442
3r5yF42Uncharacterized protein/0.442
3vg9ZMAAdenosine receptor A2a/0.442
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4hr2ADPNucleoside diphosphate kinase/0.442
4id5T27Gag-Pol polyprotein2.7.7.490.442
4n4v2GYTankyrase-12.4.2.300.442
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.442
1ek2CDUBifunctional epoxide hydrolase 2/0.441
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.441
3q44D50M1 family aminopeptidase3.4.110.441
3w0tHPULactoylglutathione lyase4.4.1.50.441
4dm6TTBRetinoic acid receptor beta/0.441
4elb34SDihydrofolate reductase/0.441
4ele31IDihydrofolate reductase/0.441
4rvfTYDD-mycarose 3-C-methyltransferase/0.441
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.441
5kgpACOPredicted acetyltransferase/0.441
5iu86DZAdenosine receptor A2a/0.441
1an5CB3Thymidylate synthase/0.440
1bzfTMQDihydrofolate reductase1.5.1.30.440
1dhjMTXDihydrofolate reductase1.5.1.30.440
1disBDMDihydrofolate reductase1.5.1.30.440
1g6oADPCag alpha/0.440
1kqgHQOFormate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit/0.440
1o6qR17Squalene--hopene cyclase4.2.1.1290.440
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.440
1zg32HIIsoflavone 4'-O-methyltransferase/0.440
2wvmGDDMannosyl-3-phosphogylcerate synthase/0.440
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.440
4gn6TYLLactoperoxidase1.11.1.70.440
4jvj1MVFarnesyl pyrophosphate synthase2.5.1.100.440
4lcg1WMUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.440
4pnmNU1Tankyrase-22.4.2.300.440
4qzuRTLRetinol-binding protein 2/0.440
4x5jFOLDihydrofolate reductase1.5.1.30.440
5dldUD1UDP-N-Acetylglucosamine 2-epimerase/0.440
5jtbZMAAdenosine receptor A2a/0.440