Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3be2RAJVascular endothelial growth factor receptor 22.7.10.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3be2RAJVascular endothelial growth factor receptor 22.7.10.11.000
3b8q900Vascular endothelial growth factor receptor 22.7.10.10.578
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.568
4equG6ISerine/threonine-protein kinase 102.7.11.10.554
4tyj0LIFibroblast growth factor receptor 42.7.10.10.546
4agwNG7Proto-oncogene tyrosine-protein kinase Src2.7.10.20.545
2p2h994Vascular endothelial growth factor receptor 22.7.10.10.544
2bakAQZMitogen-activated protein kinase 14/0.541
4a9yAQZMitogen-activated protein kinase 14/0.541
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.527
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.522
2i1m5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.522
2og81N8Tyrosine-protein kinase Lck2.7.10.20.521
3ctj320Hepatocyte growth factor receptor2.7.10.10.518
3hv3R49Mitogen-activated protein kinase 14/0.517
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.517
4qrc0LIFibroblast growth factor receptor 42.7.10.10.517
1x8b824Wee1-like protein kinase2.7.10.20.515
3lfeZ84Mitogen-activated protein kinase 14/0.511
4k9yK9YFocal adhesion kinase 12.7.10.20.500
2z2w770Wee1-like protein kinase2.7.10.20.497
3biz61EWee1-like protein kinase2.7.10.20.497
4kaoKAOFocal adhesion kinase 12.7.10.20.494
2oh4GIGVascular endothelial growth factor receptor 22.7.10.10.493
3cth319Hepatocyte growth factor receptor2.7.10.10.493
4rh10TTSpore photoproduct lyase/0.491
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.490
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.490
3dkoIHZEphrin type-A receptor 72.7.10.10.489
2in6839Wee1-like protein kinase2.7.10.20.488
3bi6396Wee1-like protein kinase2.7.10.20.488
3cr0809Wee1-like protein kinase2.7.10.20.486
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.485
4h1j0YHProtein-tyrosine kinase 2-beta2.7.10.20.485
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.483
3qri919Tyrosine-protein kinase ABL12.7.10.20.482
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.481
2y6o1N1Ephrin type-A receptor 42.7.10.10.480
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.480
4c8b0LIReceptor-interacting serine/threonine-protein kinase 22.7.11.10.480
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.480
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.478
2io6330Wee1-like protein kinase2.7.10.20.478
3gcq1BUMitogen-activated protein kinase 14/0.478
3p9tTCLRepressor/0.478
3tubFPUTyrosine-protein kinase SYK2.7.10.20.478
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.478
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.478
2dq7STUTyrosine-protein kinase Fyn2.7.10.20.477
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.477
3cqeP91Wee1-like protein kinase2.7.10.20.477
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.477
1m52P17Tyrosine-protein kinase ABL12.7.10.20.476
3b8r887Vascular endothelial growth factor receptor 22.7.10.10.476
2ivuZD6Proto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.475
3vo30KFVascular endothelial growth factor receptor 22.7.10.10.475
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.474
5iubCLRAdenosine receptor A2a/0.474
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.473
3d74NBBPheromone-binding protein ASP1/0.472
3fzt4JZProtein-tyrosine kinase 2-beta2.7.10.20.471
2jedLG8Protein kinase C theta type2.7.11.130.470
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
1og5SWFCytochrome P450 2C9/0.469
3eta351Insulin receptor2.7.10.10.469
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.469
3s4qNK0Mitogen-activated protein kinase 14/0.468
4hni16WCasein kinase I isoform epsilon2.7.11.10.468
4qa2SHHHistone deacetylase 83.5.1.980.468
3zewSTUEphrin type-B receptor 42.7.10.10.467
5dp2NAPCurF/0.467
1mewXMPInosine-5'-monophosphate dehydrogenase/0.466
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.466
4y93746Tyrosine-protein kinase/0.466
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.465
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.464
2ewaSB2Mitogen-activated protein kinase 14/0.464
4fnyI3KALK tyrosine kinase receptor2.7.10.10.464
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.464
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.463
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.463
4bkjSTIEpithelial discoidin domain-containing receptor 12.7.10.10.463
4j6dTESCytochrome P450 monooxygenase/0.463
3qm4PN0Cytochrome P450 2D6/0.462
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
2yg4FADPutrescine oxidase/0.461
3d73NBBPheromone-binding protein ASP1/0.461
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.461
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.460
3ue4DB8Tyrosine-protein kinase ABL12.7.10.20.460
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.459
4gk2L66Ephrin type-A receptor 32.7.10.10.459
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
2vd0D27Hematopoietic prostaglandin D synthase/0.458
3h3r14HCollagen type IV alpha-3-binding protein/0.458
3njoPYVAbscisic acid receptor PYR1/0.458
3qlg1N1Proto-oncogene tyrosine-protein kinase Src2.7.10.20.458
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.458
1uhlMEIRetinoic acid receptor RXR-beta/0.457
2yn8STUEphrin type-B receptor 42.7.10.10.457
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.457
4y95746Tyrosine-protein kinase/0.457
2xvw9NRSerum albumin/0.456
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
3slkNDPPolyketide synthase extender module 2/0.456
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
4twnB96Ephrin type-A receptor 32.7.10.10.456
5k2cZMAAdenosine receptor A2a/0.456
5k2dZMAAdenosine receptor A2a/0.456
3uzaT4GAdenosine receptor A2a/0.456
1pkfEPDEpothilone C/D epoxidase1.140.455
2po7CHDFerrochelatase, mitochondrial4.99.1.10.455
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.455
3ac1KZITyrosine-protein kinase Lck2.7.10.20.455
3ac2KSETyrosine-protein kinase Lck2.7.10.20.455
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.455
4j6cSTRCytochrome P450 monooxygenase/0.455
4qa0SHHHistone deacetylase 83.5.1.980.455
3qakUKAAdenosine receptor A2a/0.455
1qpdSTUTyrosine-protein kinase Lck2.7.10.20.454
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.454
2ayp43ASerine/threonine-protein kinase Chk12.7.11.10.454
2hk51BMTyrosine-protein kinase HCK2.7.10.20.454
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.454
3uzcT4EAdenosine receptor A2a/0.454
1x2hLPALipoate-protein ligase A6.3.1.200.453
2hxzH7JCathepsin S3.4.22.270.453
2ofv242Tyrosine-protein kinase Lck2.7.10.20.453
2qo9ANPEphrin type-A receptor 32.7.10.10.453
2vwx7X4Ephrin type-B receptor 42.7.10.10.453
2zm1KSFTyrosine-protein kinase Lck2.7.10.20.453
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4jbtASDCytochrome P450 monooxygenase/0.453
5ckwANPUncharacterized protein/0.453
5jtbZMAAdenosine receptor A2a/0.453
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.452
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
1s7gNADNAD-dependent protein deacylase 2/0.451
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.451
3ad6KSCTyrosine-protein kinase Lck2.7.10.20.451
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.451
3pjcPJCTyrosine-protein kinase JAK32.7.10.20.451
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3vid4TTVascular endothelial growth factor receptor 22.7.10.10.451
3zze6XPHepatocyte growth factor receptor2.7.10.10.451
1xddAAYIntegrin alpha-L/0.450
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.450
3c34KAIGlutamate receptor ionotropic, kainate 1/0.450
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3fzsB96Protein-tyrosine kinase 2-beta2.7.10.20.450
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.450
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.450
5k2aZMAAdenosine receptor A2a/0.450
2bxoOPBSerum albumin/0.449
2hkoFADLysine-specific histone demethylase 1A10.449
3ac5KZMTyrosine-protein kinase Lck2.7.10.20.449
3cjgKIMVascular endothelial growth factor receptor 22.7.10.10.449
3e5aVX6Aurora kinase A2.7.11.10.449
3el7PD3Proto-oncogene tyrosine-protein kinase Src2.7.10.20.449
4gk3L87Ephrin type-A receptor 32.7.10.10.449
3bfa9ODOdorant binding protein ASP1/0.448
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.448
4mxoDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.448
5k2bZMAAdenosine receptor A2a/0.448
1blzACVIsopenicillin N synthase1.21.3.10.447
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2bdjHETProto-oncogene tyrosine-protein kinase Src2.7.10.20.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4fhd0TTSpore photoproduct lyase/0.447
4klrCHDFerrochelatase, mitochondrial4.99.1.10.447
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.446
2xyuQ9GEphrin type-A receptor 42.7.10.10.446
2yac937Serine/threonine-protein kinase PLK12.7.11.210.446
3cjfSAVVascular endothelial growth factor receptor 22.7.10.10.446
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.446
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4gm4TZDBenzoylformate decarboxylase4.1.1.70.446
1s4eADPGalactokinase/0.445
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2dw4FADLysine-specific histone demethylase 1A10.445
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.445
2hog710Serine/threonine-protein kinase Chk12.7.11.10.445
2of2547Tyrosine-protein kinase Lck2.7.10.20.445
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.445
3fkoFKOMitogen-activated protein kinase 14/0.445
3vs3VSETyrosine-protein kinase HCK2.7.10.20.445
4f640S8Fibroblast growth factor receptor 1/0.445
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.445
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.445
5iu86DZAdenosine receptor A2a/0.445
1uv5BRWGlycogen synthase kinase-3 beta2.7.11.260.444
2g2fAGSTyrosine-protein kinase ABL12.7.10.20.444
2gvcFADThiol-specific monooxygenase1.14.130.444
2i0ePDSProtein kinase C beta type2.7.11.130.444
2j7t274Serine/threonine-protein kinase 102.7.11.10.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3ns2PYVAbscisic acid receptor PYL2/0.444
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4ktkKTKCytochrome P450/0.444
4rtbSAMPutative thiazole biosynthesis protein ThiH/0.444
4xbfFADLysine-specific histone demethylase 1A10.444
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.444
5iu4ZMAAdenosine receptor A2a/0.444
3rfmCFFAdenosine receptor A2a/0.444
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.443
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.443
2hcdBIVVitamin D3 receptor A/0.443
2x7gPVBSRSF protein kinase 22.7.11.10.443
3ds6A17Mitogen-activated protein kinase 14/0.443
4wa9AXITyrosine-protein kinase ABL12.7.10.20.443
2owb626Serine/threonine-protein kinase PLK12.7.11.210.442
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3v94WYQPhosphodiesterase/0.442
4c62XWWTyrosine-protein kinase JAK2/0.442
4qmxH8HSerine/threonine-protein kinase 242.7.11.10.442
1ad5ANPTyrosine-protein kinase HCK2.7.10.20.441
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.441
3d4bDZDNAD-dependent protein deacetylase/0.441
4acc7YGGlycogen synthase kinase-3 beta2.7.11.260.441
5uviZMAAdenosine receptor A2a/0.441
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
1fgiSU1Fibroblast growth factor receptor 1/0.440
1n71COAAac(6')-Ii protein/0.440
2ejzSAHDiphthine synthase/0.440
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.440
3b2w9NHTyrosine-protein kinase Lck2.7.10.20.440
3c35KAIGlutamate receptor ionotropic, kainate 1/0.440
3l8sBFFMitogen-activated protein kinase 14/0.440
3p2oNADBifunctional protein FolD/0.440
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.440
4fszHK8Serine/threonine-protein kinase Chk12.7.11.10.440