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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
1w2cANPInositol-trisphosphate 3-kinase A2.7.1.127

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1w2cANPInositol-trisphosphate 3-kinase A2.7.1.1271.000
1w2dADPInositol-trisphosphate 3-kinase A2.7.1.1270.620
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.491
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.485
3cqeP91Wee1-like protein kinase2.7.10.20.479
3dqwAGSProto-oncogene tyrosine-protein kinase Src2.7.10.20.477
1hk4T44Serum albumin/0.470
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.469
2punACPMethylthioribose kinase2.7.1.1000.468
3lfcZ86Mitogen-activated protein kinase 14/0.468
2bakAQZMitogen-activated protein kinase 14/0.466
4a9yAQZMitogen-activated protein kinase 14/0.466
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.465
1fr8GDUBeta-1,4-galactosyltransferase 1/0.464
3dkoIHZEphrin type-A receptor 72.7.10.10.464
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.464
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.461
3hziATPSerine/threonine-protein kinase toxin HipA/0.461
3reyXACAdenosine receptor A2a/0.461
4k9yK9YFocal adhesion kinase 12.7.10.20.460
1l8qADPChromosomal replication initiator protein DnaA/0.459
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.459
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.458
2q70DC8Estrogen receptor/0.458
3d74NBBPheromone-binding protein ASP1/0.457
4equG6ISerine/threonine-protein kinase 102.7.11.10.457
2x9vTMQPteridine reductase/0.456
2xf3J01Uncharacterized protein/0.456
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.456
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.455
5ckwANPUncharacterized protein/0.455
3emlZMAAdenosine receptor A2a/0.455
2pl0STITyrosine-protein kinase Lck2.7.10.20.454
3htjETEbrA repressor/0.454
3lfeZ84Mitogen-activated protein kinase 14/0.454
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.454
3tptADPSerine/threonine-protein kinase toxin HipA/0.454
4o4fATPKinase/0.454
4pl9ADPEthylene receptor 1/0.454
5jtbZMAAdenosine receptor A2a/0.454
3ba6AN2Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.453
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.452
2cdcNAPGlucose 1-dehydrogenase/0.452
3qlrNDPDihydrofolate reductase1.5.1.30.452
3s41S41Glucokinase2.7.1.20.452
4h1j0YHProtein-tyrosine kinase 2-beta2.7.10.20.452
3uzcT4EAdenosine receptor A2a/0.452
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.451
3gwfNAPCyclohexanone monooxygenase/0.451
3zs5SB2Mitogen-activated protein kinase 14/0.451
4fhf0TTSpore photoproduct lyase/0.451
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
1xmmM7Gm7GpppX diphosphatase3.6.1.590.450
2x1eX1EAcyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form2.3.1.1640.450
3zlmANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.450
2pupADPMethylthioribose kinase2.7.1.1000.449
2z4sADPChromosomal replication initiator protein DnaA/0.449
3c35KAIGlutamate receptor ionotropic, kainate 1/0.449
4h9753SDihydrofolate reductase1.5.1.30.449
5k2aZMAAdenosine receptor A2a/0.449
1m79MQ1Dihydrofolate reductase1.5.1.30.448
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
3gcq1BUMitogen-activated protein kinase 14/0.448
3zsgT75Mitogen-activated protein kinase 14/0.448
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
4ixd1HVIntegrin alpha-L/0.448
5uviZMAAdenosine receptor A2a/0.448
3uzaT4GAdenosine receptor A2a/0.448
1vj3TABDihydrofolate reductase1.5.1.30.447
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
3upyFOMOxidoreductase, putative/0.447
4h9506UDihydrofolate reductase1.5.1.30.447
4h9614QDihydrofolate reductase1.5.1.30.447
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.446
1kijNOVDNA gyrase subunit B/0.446
1m7aMQUDihydrofolate reductase1.5.1.30.446
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3hx3RETRetinaldehyde-binding protein 1/0.446
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
5k2cZMAAdenosine receptor A2a/0.446
1e2jTHMThymidine kinase/0.445
2vbpVB1Isopenicillin N synthase1.21.3.10.445
2vd0D27Hematopoietic prostaglandin D synthase/0.445
3eej53RUncharacterized protein/0.445
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.445
3vi7CBDHematopoietic prostaglandin D synthase/0.445
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4iaq2GM5-hydroxytryptamine receptor 1B/0.445
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.445
4uofDATNucleoside diphosphate kinase/0.445
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
1zydATPeIF-2-alpha kinase GCN2/0.444
2bfpH4BPteridine reductase 11.5.1.330.444
2fziDH3Dihydrofolate reductase1.5.1.30.444
2oh4GIGVascular endothelial growth factor receptor 22.7.10.10.444
2p4iMR9Angiopoietin-1 receptor2.7.10.10.444
2ydoADNAdenosine receptor A2a/0.444
2z7gEH9Adenosine deaminase3.5.4.40.444
3tubFPUTyrosine-protein kinase SYK2.7.10.20.444
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
4f0fACPProbable serine/threonine-protein kinase roco42.7.11.10.444
1i59ADPChemotaxis protein CheA2.7.13.30.443
1og5SWFCytochrome P450 2C9/0.443
1x7gNAPPutative ketoacyl reductase1.3.10.443
2bnsMSTReaction center protein L chain/0.443
2j5xGSPADP-ribosylation factor 6/0.443
2og81N8Tyrosine-protein kinase Lck2.7.10.20.443
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.443
3p9tTCLRepressor/0.443
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.443
4e37NDPCatalase1.11.1.60.443
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.443
1hfqMOTDihydrofolate reductase1.5.1.30.442
2ewaSB2Mitogen-activated protein kinase 14/0.442
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.442
3fzt4JZProtein-tyrosine kinase 2-beta2.7.10.20.442
3iw8HIZMitogen-activated protein kinase 14/0.442
3jrxS1AAcetyl-CoA carboxylase 2/0.442
4ffmADPUncharacterized protein/0.442
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.441
1ezfIN0Squalene synthase2.5.1.210.441
1p8dCO1Oxysterols receptor LXR-beta/0.441
2jblSMAReaction center protein L chain/0.441
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.441
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.441
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.441
3h4vDVPPteridine reductase 11.5.1.330.441
3njoPYVAbscisic acid receptor PYR1/0.441
4bfwZVWPantothenate kinase2.7.1.330.441
5kf2COAPredicted acetyltransferase/0.441
1aoeGW3Dihydrofolate reductase1.5.1.30.440
1i58ACPChemotaxis protein CheA2.7.13.30.440
1ly4COQDihydrofolate reductase1.5.1.30.440
1m78CLZDihydrofolate reductase1.5.1.30.440
1t8xPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.440
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2qe4JJ3Estrogen receptor/0.440
2x20PIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.440
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.440
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.440
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.440
5k2bZMAAdenosine receptor A2a/0.440