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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
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.11.000
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.580
2xnn430Serine/threonine-protein kinase Nek22.7.11.10.577
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.571
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.570
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.565
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.560
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.535
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.535
2yac937Serine/threonine-protein kinase PLK12.7.11.210.532
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.531
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.524
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.513
4h1j0YHProtein-tyrosine kinase 2-beta2.7.10.20.511
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.504
3qakUKAAdenosine receptor A2a/0.503
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.502
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.501
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.501
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.500
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.500
3cr0809Wee1-like protein kinase2.7.10.20.497
4f1oACPProbable serine/threonine-protein kinase roco42.7.11.10.496
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.491
3rfmCFFAdenosine receptor A2a/0.491
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.489
4j6cSTRCytochrome P450 monooxygenase/0.489
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.487
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.485
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.484
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.484
3uzcT4EAdenosine receptor A2a/0.484
2in6839Wee1-like protein kinase2.7.10.20.483
2io6330Wee1-like protein kinase2.7.10.20.481
4fnyI3KALK tyrosine kinase receptor2.7.10.10.478
3cqeP91Wee1-like protein kinase2.7.10.20.477
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.476
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.476
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.476
3fowIMHPurine nucleoside phosphorylase/0.474
1dr4HBIDihydrofolate reductase1.5.1.30.472
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.472
3reyXACAdenosine receptor A2a/0.472
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.471
4j6dTESCytochrome P450 monooxygenase/0.469
4m2xTMQDihydrofolate reductase1.5.1.30.468
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.467
3eigMTXDihydrofolate reductase1.5.1.30.466
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.466
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.465
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.465
2z4sADPChromosomal replication initiator protein DnaA/0.465
3p2oNADBifunctional protein FolD/0.465
1ygkRRCPyridoxal kinase2.7.1.350.464
1zydATPeIF-2-alpha kinase GCN2/0.464
3fzsB96Protein-tyrosine kinase 2-beta2.7.10.20.464
3h4vDVPPteridine reductase 11.5.1.330.464
3issEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.464
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.464
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.463
3biz61EWee1-like protein kinase2.7.10.20.462
4b99R4LMitogen-activated protein kinase 72.7.11.240.462
4iaq2GM5-hydroxytryptamine receptor 1B/0.461
4k9yK9YFocal adhesion kinase 12.7.10.20.461
3pqbVGPPutative oxidoreductase/0.460
4lv8ADPRhoptry protein 5 C/0.460
3pwhZMAAdenosine receptor A2a/0.460
1pkfEPDEpothilone C/D epoxidase1.140.459
1w2cANPInositol-trisphosphate 3-kinase A2.7.1.1270.459
2owb626Serine/threonine-protein kinase PLK12.7.11.210.459
1fgiSU1Fibroblast growth factor receptor 1/0.458
1pr5TBNPurine nucleoside phosphorylase DeoD-type/0.458
2c97JCL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
2og81N8Tyrosine-protein kinase Lck2.7.10.20.458
3lfeZ84Mitogen-activated protein kinase 14/0.458
3zsh469Mitogen-activated protein kinase 14/0.458
4jlm1NNDeoxycytidine kinase2.7.1.740.458
5bn4ANPV-type ATP synthase alpha chain/0.458
1u0hONMAdenylate cyclase type 2/0.457
1u0hONMAdenylate cyclase type 5/0.457
2bfpH4BPteridine reductase 11.5.1.330.457
3fzt4JZProtein-tyrosine kinase 2-beta2.7.10.20.457
3n0yAPCAdenylate cyclase 2/0.457
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.457
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.457
1e92HBIPteridine reductase 11.5.1.330.456
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.456
1oi9N20Cyclin-dependent kinase 22.7.11.220.455
1tezHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.455
2bfmTOPPteridine reductase 11.5.1.330.455
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.455
3cth319Hepatocyte growth factor receptor2.7.10.10.455
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.455
1ove358Mitogen-activated protein kinase 14/0.454
1ygjRMCPyridoxal kinase2.7.1.350.454
3vf60H6Glucokinase2.7.1.20.454
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.454
1dg7WRBDihydrofolate reductase1.5.1.30.453
2giuFBREstrogen receptor beta/0.453
3vt7VDXVitamin D3 receptor/0.453
4at0FADPossible succinate dehydrogenase/0.453
4h3g10QBeta-secretase 13.4.23.460.453
4j6bPLOCytochrome P450 monooxygenase/0.453
1w7h3IPMitogen-activated protein kinase 14/0.452
3p3zP3ZPutative cytochrome P450/0.452
1kijNOVDNA gyrase subunit B/0.451
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.451
2gfsPQBMitogen-activated protein kinase 14/0.451
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.451
3kqjUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.451
3lthUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.451
4gg70J8Hepatocyte growth factor receptor2.7.10.10.451
1ia4TQ6Dihydrofolate reductase1.5.1.30.450
2oh4GIGVascular endothelial growth factor receptor 22.7.10.10.450
2zsdCOAPantothenate kinase2.7.1.330.450
3c35KAIGlutamate receptor ionotropic, kainate 1/0.450
3d4bDZDNAD-dependent protein deacetylase/0.450
3ewrAPRReplicase polyprotein 1a3.4.220.450
3i64DNA2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase/0.450
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
4jbtASDCytochrome P450 monooxygenase/0.450
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
5ckwANPUncharacterized protein/0.450
1hfqMOTDihydrofolate reductase1.5.1.30.449
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.449
1xzqFONtRNA modification GTPase MnmE3.6.50.449
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.449
4deg0JJHepatocyte growth factor receptor2.7.10.10.449
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.449
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.449
2bf7HBIPteridine reductase 11.5.1.330.448
2qeiCXXNa(+):neurotransmitter symporter (Snf family)/0.448
2rl2UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.448
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.448
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.448
3eon341Glutaryl-CoA dehydrogenase/0.448
3n0z3ATAdenylate cyclase 2/0.448
4g1nNZTPyruvate kinase PKM2.7.1.400.448
4hni16WCasein kinase I isoform epsilon2.7.11.10.448
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.448
5ab6CAANonspecific lipid-transfer protein, putative/0.448
2c4cFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.447
2p1v5TNRetinoic acid receptor RXR-alpha/0.447
2zs8ADPPantothenate kinase2.7.1.330.447
3clbTMQBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.447
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.447
1m7bGTPRho-related GTP-binding protein RhoE/0.446
1zy5ANPeIF-2-alpha kinase GCN2/0.446
2cjfRP43-dehydroquinate dehydratase4.2.1.100.446
3c10TSNHistone deacetylase 73.5.1.980.446
3vi7CBDHematopoietic prostaglandin D synthase/0.446
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.446
4ddrMMVDihydrofolate reductase1.5.1.30.446
4hfp15UProthrombin3.4.21.50.446
5c1mCLRMu-type opioid receptor/0.446
1yhjR6CPyridoxal kinase2.7.1.350.445
2z2w770Wee1-like protein kinase2.7.10.20.445
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.445
3ix4TX1Transcriptional activator protein LasR/0.445
4bdoKAIGlutamate receptor ionotropic, kainate 2/0.445
4bfyZVYPantothenate kinase2.7.1.330.445
4kbn25UDihydrofolate reductase1.5.1.30.445
4xg1LLPDiaminopimelate decarboxylase/0.445
1w7kADPDihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.444
2dvlFADAcyl-CoA dehydrogenase/0.444
2wo7ASVIsopenicillin N synthase1.21.3.10.444
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4bfsZVSPantothenate kinase2.7.1.330.444
4jva1ORcAMP-dependent protein kinase type II-beta regulatory subunit/0.444
4kfj1R0Dihydrofolate reductase1.5.1.30.444
5uviZMAAdenosine receptor A2a/0.444
1mc5AHEAlcohol dehydrogenase class-31.1.1.10.443
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.443
2dqsTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.443
2ed3SAHDiphthine synthase/0.443
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.443
2punACPMethylthioribose kinase2.7.1.1000.443
2v57PRLTetR family transcriptional regulator/0.443
2vbpVB1Isopenicillin N synthase1.21.3.10.443
2vczVC3Hematopoietic prostaglandin D synthase/0.443
2x7hPFNProstaglandin reductase 310.443
3abaFLICytochrome P450/0.443
3bqdDAYGlucocorticoid receptor/0.443
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.443
3d5wADPSerine/threonine-protein kinase PLK/0.443
3dfrMTXDihydrofolate reductase1.5.1.30.443
3dgeADPSensor histidine kinase/0.443
3ge7AFQQueuine tRNA-ribosyltransferase2.4.2.290.443
3i587NA2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase/0.443
3qls55VDihydrofolate reductase1.5.1.30.443
3qlwN22Dihydrofolate reductase1.5.1.30.443
3rsv3RSBeta-secretase 13.4.23.460.443
3ufvHW9Nitric oxide synthase, brain1.14.13.390.443
4dbc3QPAspartate aminotransferase2.6.1.10.443
4jlj1NMDeoxycytidine kinase2.7.1.740.443
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.443
5g53NECAdenosine receptor A2a/0.443
1ivrCBAAspartate aminotransferase, mitochondrial2.6.1.10.442
1je1GMPPurine nucleoside phosphorylase/0.442
2a4xBLMMitomycin-binding protein/0.442
2a9z26AAdenosine kinase2.7.1.200.442
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.442
3fkoFKOMitogen-activated protein kinase 14/0.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
3jwcEKBDihydrofolate reductase/0.442
3sl2ATPSensor histidine kinase WalK/0.442
3zc5W9ZHepatocyte growth factor receptor2.7.10.10.442
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.442
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.442
4ivrN50Thymidine kinase/0.442
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.442
4wboANWRhodopsin kinase/0.442
5iua6DXAdenosine receptor A2a/0.442
3uzaT4GAdenosine receptor A2a/0.442
1bzfTMQDihydrofolate reductase1.5.1.30.441
1krv147Galactoside O-acetyltransferase2.3.1.180.441
1oc1ASVIsopenicillin N synthase1.21.3.10.441
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
1v0pPVBCell division control protein 2 homolog2.7.11.220.441
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.441
2chw039Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
2ewaSB2Mitogen-activated protein kinase 14/0.441
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.441
2o98FSC14-3-3-like protein C/0.441
2ph5NADHomospermidine synthase/0.441
2wgjVGHHepatocyte growth factor receptor2.7.10.10.441
3zkyWT4Isopenicillin N synthase1.21.3.10.441
4bwaN0BPyrrolysine--tRNA ligase/0.441
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.441
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.441
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
1ir3ANPInsulin receptor2.7.10.10.440
1pd8CO4Dihydrofolate reductase1.5.1.30.440
1w83L11Mitogen-activated protein kinase 14/0.440
2g78REACellular retinoic acid-binding protein 2/0.440
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.440
3hub469Mitogen-activated protein kinase 14/0.440
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.440
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
4ap1NAPSteroid monooxygenase/0.440
4ib4ERM5-hydroxytryptamine receptor 2B/0.440
4r20AERCytochrome P450 family 17 polypeptide 2/0.440
4tx9AMZPhosphoribosyl isomerase A/0.440
4u0k744Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
5k2cZMAAdenosine receptor A2a/0.440
5k2aZMAAdenosine receptor A2a/0.440