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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
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.11.000
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.658
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.625
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.622
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.578
2yac937Serine/threonine-protein kinase PLK12.7.11.210.563
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.561
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.553
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.552
2z2w770Wee1-like protein kinase2.7.10.20.550
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.548
2in6839Wee1-like protein kinase2.7.10.20.546
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.546
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.544
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.542
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.540
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.539
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.539
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.535
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.535
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.535
2xnn430Serine/threonine-protein kinase Nek22.7.11.10.530
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.527
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.525
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.524
3biz61EWee1-like protein kinase2.7.10.20.524
1x8b824Wee1-like protein kinase2.7.10.20.523
2owb626Serine/threonine-protein kinase PLK12.7.11.210.523
2io6330Wee1-like protein kinase2.7.10.20.520
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.516
3cr0809Wee1-like protein kinase2.7.10.20.516
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.515
3cqeP91Wee1-like protein kinase2.7.10.20.493
4ea2RWZDehydrosqualene synthase/0.492
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.490
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.489
1hb1OCVIsopenicillin N synthase1.21.3.10.484
2y6fM9FIsopenicillin N synthase1.21.3.10.484
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.481
3cgyRDCVirulence sensor histidine kinase PhoQ2.7.13.30.480
3qm4PN0Cytochrome P450 2D6/0.480
2ydoADNAdenosine receptor A2a/0.479
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.479
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.478
3zkyWT4Isopenicillin N synthase1.21.3.10.478
1blzACVIsopenicillin N synthase1.21.3.10.477
1diuBDMDihydrofolate reductase1.5.1.30.477
4f0fACPProbable serine/threonine-protein kinase roco42.7.11.10.476
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.476
1m9k7NINitric oxide synthase, endothelial1.14.13.390.475
2bf7HBIPteridine reductase 11.5.1.330.474
3bi6396Wee1-like protein kinase2.7.10.20.474
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.474
4jv41ORcAMP-dependent protein kinase type I-alpha regulatory subunit/0.474
4iah1DXAlr2278 protein/0.473
2vbdV10Isopenicillin N synthase1.21.3.10.472
1p8dCO1Oxysterols receptor LXR-beta/0.471
1pkfEPDEpothilone C/D epoxidase1.140.471
1xuoLA1Integrin alpha-L/0.471
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.471
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.471
1m9m6NINitric oxide synthase, endothelial1.14.13.390.470
2bfaCB3Pteridine reductase 11.5.1.330.470
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.469
4b4w9L9Bifunctional protein FolD/0.469
1q5dEPBEpothilone C/D epoxidase1.140.468
3iktNADRedox-sensing transcriptional repressor Rex/0.467
1bk0ACVIsopenicillin N synthase1.21.3.10.466
1dr4HBIDihydrofolate reductase1.5.1.30.466
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.466
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.466
4b4vL34Bifunctional protein FolD/0.466
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.465
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.465
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.464
2iviACWIsopenicillin N synthase1.21.3.10.464
3b04OOPIsopentenyl-diphosphate delta-isomerase/0.464
3gcq1BUMitogen-activated protein kinase 14/0.463
1w06W05Isopenicillin N synthase1.21.3.10.462
2jb4A14Isopenicillin N synthase1.21.3.10.462
3cv9VDXVitamin D3 dihydroxylase/0.462
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.461
2fzjDH3Dihydrofolate reductase1.5.1.30.461
4iae1DXAlr2278 protein/0.461
1e92HBIPteridine reductase 11.5.1.330.460
3ctj320Hepatocyte growth factor receptor2.7.10.10.460
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.459
3h4vDVPPteridine reductase 11.5.1.330.459
4bb3KKAIsopenicillin N synthase1.21.3.10.459
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.458
3d5wADPSerine/threonine-protein kinase PLK/0.458
3ewsADPATP-dependent RNA helicase DDX19B3.6.4.130.458
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.457
2vbpVB1Isopenicillin N synthase1.21.3.10.457
3c36KAIGlutamate receptor ionotropic, kainate 1/0.457
1hb3SCVIsopenicillin N synthase1.21.3.10.456
1ohkCOPDihydrofolate reductase1.5.1.30.456
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.456
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.455
3c1xCKKHepatocyte growth factor receptor2.7.10.10.455
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3zoiM2WIsopenicillin N synthase1.21.3.10.455
4djx0KQBeta-secretase 13.4.23.460.455
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.454
1qjfACSIsopenicillin N synthase1.21.3.10.454
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.454
3wsbRWZFarnesyltransferase, putative/0.454
3zloX8UBcl-2-like protein 1/0.454
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.453
3arvSAUChitinase A/0.453
3s41S41Glucokinase2.7.1.20.453
4twnB96Ephrin type-A receptor 32.7.10.10.453
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.452
1w7h3IPMitogen-activated protein kinase 14/0.452
2h94FADLysine-specific histone demethylase 1A10.452
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.452
4zhiADPKinesin-like protein KIF11/0.452
1dr3HBIDihydrofolate reductase1.5.1.30.451
1oc1ASVIsopenicillin N synthase1.21.3.10.451
1u0hONMAdenylate cyclase type 2/0.451
1u0hONMAdenylate cyclase type 5/0.451
2pauD5M5'-deoxynucleotidase YfbR/0.451
4equG6ISerine/threonine-protein kinase 102.7.11.10.451
4kfj1R0Dihydrofolate reductase1.5.1.30.451
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2b378PSEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2bfpH4BPteridine reductase 11.5.1.330.450
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.450
3cth319Hepatocyte growth factor receptor2.7.10.10.450
4at0FADPossible succinate dehydrogenase/0.450
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.449
3c9tTPSThiamine-monophosphate kinase/0.449
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.449
4g1nNZTPyruvate kinase PKM2.7.1.400.449
4jqh1MFAlr2278 protein/0.449
4rh10TTSpore photoproduct lyase/0.449
3rfmCFFAdenosine receptor A2a/0.449
2xtbKRMAdenosine kinase, putative/0.448
3abaFLICytochrome P450/0.448
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.448
3c35KAIGlutamate receptor ionotropic, kainate 1/0.448
3gieACPSensor histidine kinase DesK2.7.13.30.448
4bfxZVXPantothenate kinase2.7.1.330.448
4d7eFADPutative lysine-N-oxygenase/0.448
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.447
1ia3TQ5Dihydrofolate reductase1.5.1.30.447
1mczRMNBenzoylformate decarboxylase4.1.1.70.447
3dfrMTXDihydrofolate reductase1.5.1.30.447
3ds6A17Mitogen-activated protein kinase 14/0.447
3l6jZ90Alr2278 protein/0.447
4f1oACPProbable serine/threonine-protein kinase roco42.7.11.10.447
1p33MTXPteridine reductase 11.5.1.330.446
1tl7ONMAdenylate cyclase type 2/0.446
1tl7ONMAdenylate cyclase type 5/0.446
2bfmTOPPteridine reductase 11.5.1.330.446
3fhxPXLPyridoxal kinase2.7.1.350.446
3hziATPSerine/threonine-protein kinase toxin HipA/0.446
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.446
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.446
4h1e10JBeta-secretase 13.4.23.460.446
1cqp803Integrin alpha-L/0.445
1synF89Thymidylate synthase/0.445
1uhlMEIRetinoic acid receptor RXR-beta/0.445
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.445
2olcADPMethylthioribose kinase2.7.1.1000.445
2rehFADNitroalkane oxidase1.7.3.10.445
2wd8VGFPteridine reductase/0.445
3p9tTCLRepressor/0.445
3q9bB3NAcetylpolyamine amidohydrolase/0.445
1obnASVIsopenicillin N synthase1.21.3.10.444
1tsdF89Thymidylate synthase/0.444
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2bakAQZMitogen-activated protein kinase 14/0.444
2ejzSAHDiphthine synthase/0.444
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.444
2ym6YM6Serine/threonine-protein kinase Chk12.7.11.10.444
3ckxSTUSerine/threonine-protein kinase 242.7.11.10.444
3l0lHC3Nuclear receptor ROR-gamma/0.444
4a9yAQZMitogen-activated protein kinase 14/0.444
4b2gV1NUncharacterized protein/0.444
4gt8ADPSensor protein VraS2.7.13.30.444
1t57FMNConserved protein/0.443
2dhfDZFDihydrofolate reductase1.5.1.30.443
2wo7ASVIsopenicillin N synthase1.21.3.10.443
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3v94WYQPhosphodiesterase/0.443
3vf60H6Glucokinase2.7.1.20.443
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.443
4ft0HK9Serine/threonine-protein kinase Chk12.7.11.10.443
4h3i10VBeta-secretase 13.4.23.460.443
4jauADPSensor histidine kinase/0.443
4jbtASDCytochrome P450 monooxygenase/0.443
3pwhZMAAdenosine receptor A2a/0.443
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2gfsPQBMitogen-activated protein kinase 14/0.442
2gjnFMNNitronate monooxygenase1.13.12.160.442
2gvcFADThiol-specific monooxygenase1.14.130.442
2po7CHDFerrochelatase, mitochondrial4.99.1.10.442
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.442
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.442
3dgeADPSensor histidine kinase/0.442
3fsjD7KBenzoylformate decarboxylase4.1.1.70.442
3ko0TFPProtein S100-A4/0.442
4b7754MBeta-secretase 13.4.23.460.442
4bj9UHBTankyrase-22.4.2.300.442
5k2cZMAAdenosine receptor A2a/0.442
1ndzFR5Adenosine deaminase3.5.4.40.441
2a9z26AAdenosine kinase2.7.1.200.441
2pl0STITyrosine-protein kinase Lck2.7.10.20.441
3lfeZ84Mitogen-activated protein kinase 14/0.441
3u8hBHPPhospholipase A2, membrane associated/0.441
4f6vZYMDehydrosqualene synthase/0.441
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.441
4m4821BSodium-dependent dopamine transporter/0.441
2pirDHTAndrogen receptor/0.440
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.440
2w9hTOPDihydrofolate reductase1.5.1.30.440
2x9vTMQPteridine reductase/0.440
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.440
3jx3JI5Nitric oxide synthase, brain1.14.13.390.440
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.440
3tdaPN0Cytochrome P450 2D6/0.440
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
3vi7CBDHematopoietic prostaglandin D synthase/0.440
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jlm1NNDeoxycytidine kinase2.7.1.740.440
4jvlESTEstrogen sulfotransferase2.8.2.40.440
4k9yK9YFocal adhesion kinase 12.7.10.20.440
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
5g53NECAdenosine receptor A2a/0.440