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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
3pd5TSBThreonine--tRNA ligase6.1.1.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3pd5TSBThreonine--tRNA ligase6.1.1.31.000
2hl2SSAThreonine--tRNA ligase6.1.1.30.653
2hl1A3SThreonine--tRNA ligase6.1.1.30.608
3pd4A3GThreonine--tRNA ligase6.1.1.30.580
4rrgA3TThreonine--tRNA ligase6.1.1.30.574
3pd2A3SThreonine--tRNA ligase6.1.1.30.571
4rrfA3SThreonine--tRNA ligase6.1.1.30.565
4rrqA3SThreonine--tRNA ligase6.1.1.30.565
3pd3A3TThreonine--tRNA ligase6.1.1.30.543
4rrrA3TThreonine--tRNA ligase6.1.1.30.529
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.527
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.521
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.504
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.502
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.501
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.494
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.492
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.489
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.486
2hl0A3SThreonine--tRNA ligase6.1.1.30.483
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.482
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.482
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.479
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.477
3ml9ML9Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
1r2jFADFkbI/0.473
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.473
5h8tRTLRetinol-binding protein 1/0.472
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.471
4s0vSUVOrexin receptor type 2/0.470
3q5kD1UHeat shock protein 83-1/0.468
2rhrEMOPutative ketoacyl reductase1.3.10.467
2g1pSAHDNA adenine methylase2.1.1.720.466
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.465
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.463
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.463
3gwfFADCyclohexanone monooxygenase/0.461
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.461
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.459
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.458
2p5uNADUDP-glucose 4-epimerase/0.458
3oqkS52Renin3.4.23.150.458
1bsvNDPGDP-L-fucose synthase/0.457
3mnrSD1Heat shock protein HSP 90-alpha/0.457
4rrcA3TProbable threonine--tRNA ligase 26.1.1.30.457
1fxsNAPGDP-L-fucose synthase/0.456
1uydPU8Heat shock protein HSP 90-alpha/0.456
3a783EVVitamin D3 receptor/0.456
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4l4xNDPAmphI/0.456
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.456
2wouZZFTGF-beta receptor type-12.7.11.300.454
3gu83GUDeath-associated protein kinase 12.7.11.10.454
3hz5Z64Heat shock protein HSP 90-alpha/0.454
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.454
2qg2A91Heat shock protein HSP 90-alpha/0.453
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
4fa60TAPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4gk3L87Ephrin type-A receptor 32.7.10.10.453
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.453
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.452
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3q43D66M1 family aminopeptidase3.4.110.452
4qa0SHHHistone deacetylase 83.5.1.980.452
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.451
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4iaq2GM5-hydroxytryptamine receptor 1B/0.451
4l49CAMCamphor 5-monooxygenase1.14.15.10.451
2xviFADPutative flavin-containing monooxygenase/0.450
3inxJZCHeat shock protein HSP 90-alpha/0.450
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.450
4gg70J8Hepatocyte growth factor receptor2.7.10.10.450
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.450
5iu86DZAdenosine receptor A2a/0.450
1iidNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.449
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.449
2jfaRALEstrogen receptor/0.449
2yee2ECHeat shock protein HSP 90-alpha/0.449
2z3uCRRCytochrome P450/0.449
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
5iubCLRAdenosine receptor A2a/0.449
1ju6LYAThymidylate synthase2.1.1.450.448
1uy7PU4Heat shock protein HSP 90-alpha/0.448
2fpcSCGStrictosidine synthase4.3.3.20.448
2h55DZ8Heat shock protein HSP 90-alpha/0.448
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.448
3njoP2MAbscisic acid receptor PYR1/0.448
3vrvYSDVitamin D3 receptor/0.447
4hnc0UTMandelate racemase/0.447
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4rtsSAMDNA adenine methylase2.1.1.720.447
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
3vtdTKDVitamin D3 receptor/0.446
4bgg844Activin receptor type-12.7.11.300.446
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
2wi72KLHeat shock protein HSP 90-alpha/0.445
3fr8NDPKetol-acid reductoisomerase, chloroplastic1.1.1.860.445
4m9aFDAAcyl-CoA dehydrogenase/0.445
4rtrSAMDNA adenine methylase2.1.1.720.445
1fmlRTLRetinol dehydratase/0.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.444
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.444
4uyf73BBromodomain-containing protein 2/0.444
5k2cZMAAdenosine receptor A2a/0.444
5k2bZMAAdenosine receptor A2a/0.444
1e7qNAPGDP-L-fucose synthase/0.443
3nr4PYVAbscisic acid receptor PYL2/0.443
3v49PK0Androgen receptor/0.443
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.443
5jtbZMAAdenosine receptor A2a/0.443
1j39UPGDNA beta-glucosyltransferase/0.442
1qknRALEstrogen receptor beta/0.442
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4iteTEYVitamin D3 receptor/0.442
1rk3VDXVitamin D3 receptor/0.441
1uyfPU1Heat shock protein HSP 90-alpha/0.441
2x1nX1NCyclin-dependent kinase 22.7.11.220.441
3q44D50M1 family aminopeptidase3.4.110.441
3w5tLHPVitamin D3 receptor/0.441
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.441
5dc5B3NHistone deacetylase 83.5.1.980.441
1dr3HBIDihydrofolate reductase1.5.1.30.440
1uyePU9Heat shock protein HSP 90-alpha/0.440
2ca0PXICytochrome P450 monooxygenase PikC/0.440
2hxq373Serine/threonine-protein kinase Chk12.7.11.10.440
2jlaTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.440
2kceD16Thymidylate synthase/0.440
2wi4ZZ4Heat shock protein HSP 90-alpha/0.440
2zjwREFCasein kinase II subunit alpha2.7.11.10.440
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.440
3ns2PYVAbscisic acid receptor PYL2/0.440
3w5p4OAVitamin D3 receptor/0.440
4bqpVMYEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4eiyZMAAdenosine receptor A2a/0.440
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4hy6FJ1Heat shock protein HSP 90-alpha/0.440
4itfTFYVitamin D3 receptor/0.440
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440