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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
3q2mCKISpectinomycin phosphotransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3q2mCKISpectinomycin phosphotransferase/1.000
3gcq1BUMitogen-activated protein kinase 14/0.508
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.498
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.498
4fex0TOAminoglycoside 3'-phosphotransferase AphA1-IAB/0.494
3qaqQAQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.486
3lfcZ86Mitogen-activated protein kinase 14/0.485
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.484
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.482
1e8wQUEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.480
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.480
3oafOAGDihydrofolate reductase1.5.1.30.478
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.476
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
3njoPYVAbscisic acid receptor PYR1/0.470
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.470
2ewaSB2Mitogen-activated protein kinase 14/0.468
3rfmCFFAdenosine receptor A2a/0.468
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
3t8xT8XT-cell surface glycoprotein CD1b/0.466
3u8hBHPPhospholipase A2, membrane associated/0.466
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.466
4g95OAGDihydrofolate reductase1.5.1.30.466
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.466
2chw039Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
4iarERM5-hydroxytryptamine receptor 1B/0.463
3hu2AGSTransitional endoplasmic reticulum ATPase3.6.4.60.462
4f1sF1SPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.462
4bfrJ82Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform2.7.1.1530.461
4bfvZVVPantothenate kinase2.7.1.330.461
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.461
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.461
4j6dTESCytochrome P450 monooxygenase/0.461
2wleCOAPolysialic acid O-acetyltransferase/0.460
3qm4PN0Cytochrome P450 2D6/0.460
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
4iaq2GM5-hydroxytryptamine receptor 1B/0.460
2puiADPMethylthioribose kinase2.7.1.1000.459
1l8qADPChromosomal replication initiator protein DnaA/0.458
3ctj320Hepatocyte growth factor receptor2.7.10.10.458
3cv9VDXVitamin D3 dihydroxylase/0.458
4g1z0VPVitamin D3 receptor A/0.458
4jbtASDCytochrome P450 monooxygenase/0.458
1dr3HBIDihydrofolate reductase1.5.1.30.457
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.457
1g3mPCQEstrogen sulfotransferase2.8.2.40.456
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2bakAQZMitogen-activated protein kinase 14/0.456
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4a9yAQZMitogen-activated protein kinase 14/0.456
4klnAGSTransitional endoplasmic reticulum ATPase3.6.4.60.455
3cth319Hepatocyte growth factor receptor2.7.10.10.454
4kfj1R0Dihydrofolate reductase1.5.1.30.454
3l0lHC3Nuclear receptor ROR-gamma/0.453
3p3zP3ZPutative cytochrome P450/0.453
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.452
3iw8HIZMitogen-activated protein kinase 14/0.452
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.452
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2w3aTOPDihydrofolate reductase1.5.1.30.451
4ybnFADFlavin-nucleotide-binding protein/0.451
5k2cZMAAdenosine receptor A2a/0.451
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.450
3vt65YIVitamin D3 receptor/0.450
5k2aZMAAdenosine receptor A2a/0.450
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4j6cSTRCytochrome P450 monooxygenase/0.449
1lhwESMSex hormone-binding globulin/0.448
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.448
3rl35GPMetallophosphoesterase MPPED23.10.448
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.448
1crbRTLRetinol-binding protein 1/0.447
3da24MDCarbonic anhydrase 134.2.1.10.447
3ju8NADN-succinylglutamate 5-semialdehyde dehydrogenase1.2.1.710.447
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.447
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.447
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.447
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.447
1jxzBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.446
4jqh1MFAlr2278 protein/0.446
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
2z7gEH9Adenosine deaminase3.5.4.40.445
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3sgy06WDihydrofolate reductase1.5.1.30.444
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
5bp9SAHPutative methyltransferase protein/0.444
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.443
3fmz2T1Retinol-binding protein 4/0.443
3nxyD2HDihydrofolate reductase1.5.1.30.443
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4bfsZVSPantothenate kinase2.7.1.330.443
4bftZVTPantothenate kinase2.7.1.330.443
4ixd1HVIntegrin alpha-L/0.443
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3cr7PPSAdenylyl-sulfate kinase2.7.1.250.442
1ep4S11Gag-Pol polyprotein2.7.7.490.441
2ph5NADHomospermidine synthase/0.441
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.441
3nxvD2FDihydrofolate reductase1.5.1.30.441
3p99LNPLanosterol 14-alpha-demethylase/0.441
4ej1FOLDihydrofolate reductase1.5.1.30.441
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.441
5ckwANPUncharacterized protein/0.441
1rkhVD2Vitamin D3 receptor/0.440
1u1d181Uridine phosphorylase2.4.2.30.440
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.440
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.440
3eigMTXDihydrofolate reductase1.5.1.30.440
4ele31IDihydrofolate reductase/0.440
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.440
3emlZMAAdenosine receptor A2a/0.440
3uzaT4GAdenosine receptor A2a/0.440