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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
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.11.000
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.656
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.651
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.616
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.610
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.575
2z2w770Wee1-like protein kinase2.7.10.20.574
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.574
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.572
2yac937Serine/threonine-protein kinase PLK12.7.11.210.568
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.568
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.565
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.561
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.560
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.555
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.555
2in6839Wee1-like protein kinase2.7.10.20.550
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.549
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.549
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.547
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.545
3biz61EWee1-like protein kinase2.7.10.20.540
2xnn430Serine/threonine-protein kinase Nek22.7.11.10.536
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.532
3cqeP91Wee1-like protein kinase2.7.10.20.531
3cr0809Wee1-like protein kinase2.7.10.20.531
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.530
1x8b824Wee1-like protein kinase2.7.10.20.529
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.529
2io6330Wee1-like protein kinase2.7.10.20.528
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.524
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.521
4f0fACPProbable serine/threonine-protein kinase roco42.7.11.10.512
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.510
2owb626Serine/threonine-protein kinase PLK12.7.11.210.509
3h4vDVPPteridine reductase 11.5.1.330.506
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.499
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.499
3zkyWT4Isopenicillin N synthase1.21.3.10.494
3bi6396Wee1-like protein kinase2.7.10.20.493
3ctj320Hepatocyte growth factor receptor2.7.10.10.492
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.491
2bfpH4BPteridine reductase 11.5.1.330.489
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.489
1e92HBIPteridine reductase 11.5.1.330.488
2bfmTOPPteridine reductase 11.5.1.330.488
4zhiADPKinesin-like protein KIF11/0.488
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.486
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.483
4at0FADPossible succinate dehydrogenase/0.482
4ft0HK9Serine/threonine-protein kinase Chk12.7.11.10.480
5i2hAGIO-methyltransferase family 2/0.480
2x9vTMQPteridine reductase/0.479
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.478
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.478
1yqj6NPMitogen-activated protein kinase 14/0.476
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.476
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.475
2ym7YM7Serine/threonine-protein kinase Chk12.7.11.10.475
2bfaCB3Pteridine reductase 11.5.1.330.474
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.473
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.473
4pnmNU1Tankyrase-22.4.2.300.472
2bf7HBIPteridine reductase 11.5.1.330.471
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.471
2hog710Serine/threonine-protein kinase Chk12.7.11.10.470
3s41S41Glucokinase2.7.1.20.470
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.470
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.469
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.469
4fsyHK7Serine/threonine-protein kinase Chk12.7.11.10.468
5dp2NAPCurF/0.468
2j9lATPH(+)/Cl(-) exchange transporter 5/0.467
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.467
4jv41ORcAMP-dependent protein kinase type I-alpha regulatory subunit/0.467
3cgyRDCVirulence sensor histidine kinase PhoQ2.7.13.30.466
2ivuZD6Proto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.465
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.465
3vf60H6Glucokinase2.7.1.20.465
4bkjSTIEpithelial discoidin domain-containing receptor 12.7.10.10.465
4ea2RWZDehydrosqualene synthase/0.465
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.464
4ug91EWNitric oxide synthase oxygenase1.14.13.1650.464
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.463
2rbeZMGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.463
4dhyS41Glucokinase2.7.1.20.462
4iarERM5-hydroxytryptamine receptor 1B/0.462
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.462
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.462
1e7wMTXPteridine reductase 11.5.1.330.461
2og81N8Tyrosine-protein kinase Lck2.7.10.20.461
2xf04UBSerine/threonine-protein kinase Chk12.7.11.10.461
4ux6H4BNitric oxide synthase, inducible1.14.13.390.461
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2ym3YM3Serine/threonine-protein kinase Chk12.7.11.10.460
3d84NDPDihydrofolate reductase1.5.1.30.460
3lm1LECAgglutinin alpha chain/0.460
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.460
4iae1DXAlr2278 protein/0.460
4k9yK9YFocal adhesion kinase 12.7.10.20.460
4uqsINENitric oxide synthase oxygenase1.14.13.1650.460
5k2cZMAAdenosine receptor A2a/0.460
4uhrNGIAdenosine receptor A2a/0.460
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.459
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.459
3f82353Hepatocyte growth factor receptor2.7.10.10.459
3zoiM2WIsopenicillin N synthase1.21.3.10.459
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
4f1oACPProbable serine/threonine-protein kinase roco42.7.11.10.459
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.459
4fswHK6Serine/threonine-protein kinase Chk12.7.11.10.459
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.459
1blzACVIsopenicillin N synthase1.21.3.10.458
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.458
1fwkADPHomoserine kinase2.7.1.390.458
2vcmM11Isopenicillin N synthase1.21.3.10.458
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.458
1nhkCMPNucleoside diphosphate kinase2.7.4.60.457
2r0uM54Serine/threonine-protein kinase Chk12.7.11.10.457
2vbpVB1Isopenicillin N synthase1.21.3.10.457
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.457
5hbsRTLRetinol-binding protein 1/0.457
2wkyIBCGlutamate receptor ionotropic, kainate 1/0.456
3cth319Hepatocyte growth factor receptor2.7.10.10.456
3gkjHC3Niemann-Pick C1 protein/0.456
5k2aZMAAdenosine receptor A2a/0.456
3pblETQD(3) dopamine receptor/0.456
3qakUKAAdenosine receptor A2a/0.456
2y6fM9FIsopenicillin N synthase1.21.3.10.455
3b05IPEIsopentenyl-diphosphate delta-isomerase/0.455
3ckxSTUSerine/threonine-protein kinase 242.7.11.10.455
3e5aVX6Aurora kinase A2.7.11.10.455
3njoPYVAbscisic acid receptor PYR1/0.455
3nmpPYVAbscisic acid receptor PYL2/0.455
3p0fBAUUridine phosphorylase 22.4.2.30.455
4fnyI3KALK tyrosine kinase receptor2.7.10.10.455
5g53NECAdenosine receptor A2a/0.455
2bxoOPBSerum albumin/0.454
2gvcFADThiol-specific monooxygenase1.14.130.454
2j0j4STFocal adhesion kinase 12.7.10.20.454
2ydoADNAdenosine receptor A2a/0.454
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
4bb3KKAIsopenicillin N synthase1.21.3.10.454
4ftm1HKSerine/threonine-protein kinase Chk12.7.11.10.454
4gh2HK0Serine/threonine-protein kinase Chk12.7.11.10.454
4jqeANPCasein kinase II subunit alpha2.7.11.10.454
4l17DNQGlutamate receptor 2/0.454
5ab7MLCNonspecific lipid-transfer protein, putative/0.454
1yplRA8Prothrombin3.4.21.50.453
1z4iUMP5'(3')-deoxyribonucleotidase, mitochondrial3.1.30.453
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.453
4iah1DXAlr2278 protein/0.453
5d7pAR6NAD-dependent protein deacetylase sirtuin-23.5.10.453
1fw0KAIGlutamate receptor 2/0.452
2wmqZYQSerine/threonine-protein kinase Chk12.7.11.10.452
2y60M8FIsopenicillin N synthase1.21.3.10.452
3hazFADBifunctional protein PutA/0.452
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.452
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.452
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.452
4jauADPSensor histidine kinase/0.452
4jqh1MFAlr2278 protein/0.452
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
1m8iH4BNitric oxide synthase, inducible1.14.13.390.451
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.451
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.451
1d6w00RProthrombin3.4.21.50.450
1m8hH4BNitric oxide synthase, inducible1.14.13.390.450
1odnAPVIsopenicillin N synthase1.21.3.10.450
1zosMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.450
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.450
1crbRTLRetinol-binding protein 1/0.449
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.449
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.449
2wmtZYTSerine/threonine-protein kinase Chk12.7.11.10.449
2wo7ASVIsopenicillin N synthase1.21.3.10.449
2ydiYDISerine/threonine-protein kinase Chk12.7.11.10.449
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.449
4eiyZMAAdenosine receptor A2a/0.449
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.449
1gj5130Prothrombin3.4.21.50.448
1uv5BRWGlycogen synthase kinase-3 beta2.7.11.260.448
3eta351Insulin receptor2.7.10.10.448
3llaACPMyosin heavy chain kinase A2.7.11.70.448
3ns2PYVAbscisic acid receptor PYL2/0.448
3tkh07SSerine/threonine-protein kinase Chk12.7.11.10.448
3up3XCAaceDAF-12/0.448
4hvs647Mast/stem cell growth factor receptor Kit2.7.10.10.448
4twnB96Ephrin type-A receptor 32.7.10.10.448
1dr2TAPDihydrofolate reductase1.5.1.30.447
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1t57FMNConserved protein/0.447
2oh4GIGVascular endothelial growth factor receptor 22.7.10.10.447
2qhm7CSSerine/threonine-protein kinase Chk12.7.11.10.447
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.447
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.447
4c4oNADSADH/0.447
4ixc1JDGlucokinase2.7.1.20.447
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.447
3uzaT4GAdenosine receptor A2a/0.447
1bk0ACVIsopenicillin N synthase1.21.3.10.446
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.446
2e9oA58Serine/threonine-protein kinase Chk12.7.11.10.446
2hxq373Serine/threonine-protein kinase Chk12.7.11.10.446
2i0ePDSProtein kinase C beta type2.7.11.130.446
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.446
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
3hqdANPKinesin-like protein KIF11/0.446
4uugPXGBranched-chain amino acid aminotransferase, putative/0.446
1nm6L86Prothrombin3.4.21.50.445
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.445
1vbiNADMalate/L-lactate dehydrogenase family protein/0.445
1w83L11Mitogen-activated protein kinase 14/0.445
1zgi382Prothrombin3.4.21.50.445
2ejzSAHDiphthine synthase/0.445
2jblSMAReaction center protein L chain/0.445
2wipP49Cyclin-dependent kinase 22.7.11.220.445
2xf3J01Uncharacterized protein/0.445
3b9lAZZSerum albumin/0.445
4bdhWVISerine/threonine-protein kinase Chk22.7.11.10.445
4fszHK8Serine/threonine-protein kinase Chk12.7.11.10.445
4ftn2HKSerine/threonine-protein kinase Chk12.7.11.10.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1nvrSTUSerine/threonine-protein kinase Chk12.7.11.10.444
1oc1ASVIsopenicillin N synthase1.21.3.10.444
1synF89Thymidylate synthase/0.444
2ayp43ASerine/threonine-protein kinase Chk12.7.11.10.444
2pirDHTAndrogen receptor/0.444
2xvv9DNSerum albumin/0.444
3c1xCKKHepatocyte growth factor receptor2.7.10.10.444
3eigMTXDihydrofolate reductase1.5.1.30.444
3fznD7KBenzoylformate decarboxylase4.1.1.70.444
3jq8DX3Pteridine reductase, putative/0.444
3nn6HNK6-hydroxy-L-nicotine oxidase/0.444
3sl2ATPSensor histidine kinase WalK/0.444
3vi7CBDHematopoietic prostaglandin D synthase/0.444
3zze6XPHepatocyte growth factor receptor2.7.10.10.444
4fic0ULProto-oncogene tyrosine-protein kinase Src2.7.10.20.444
4fsqHK3Serine/threonine-protein kinase Chk12.7.11.10.444
4lwbQJ8Nitric oxide synthase oxygenase1.14.13.1650.444
1mueCDDProthrombin3.4.21.50.443
1w06W05Isopenicillin N synthase1.21.3.10.443
1yhjR6CPyridoxal kinase2.7.1.350.443
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.443
2vz0D64Pteridine reductase/0.443
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.443
2ydvNECAdenosine receptor A2a/0.443
3h3sH15Collagen type IV alpha-3-binding protein/0.443
3jq9AX1Pteridine reductase, putative/0.443
4fex0TOAminoglycoside 3'-phosphotransferase AphA1-IAB/0.443
4qrc0LIFibroblast growth factor receptor 42.7.10.10.443
5iubCLRAdenosine receptor A2a/0.443
1cdeDZFPhosphoribosylglycinamide formyltransferase/0.442
1diuBDMDihydrofolate reductase1.5.1.30.442
1jxzBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.442
1og5SWFCytochrome P450 2C9/0.442
1pkfEPDEpothilone C/D epoxidase1.140.442
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
1uzwCDHIsopenicillin N synthase1.21.3.10.442
2ewaSB2Mitogen-activated protein kinase 14/0.442
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.442
2yhuWHFPteridine reductase/0.442
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.442
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
3pe13NGCasein kinase II subunit alpha2.7.11.10.442
4bfxZVXPantothenate kinase2.7.1.330.442
4equG6ISerine/threonine-protein kinase 102.7.11.10.442
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.442
4nmcFADBifunctional protein PutA/0.442
1s9qOHTEstrogen-related receptor gamma/0.441
1u0wSTLChalcone synthase 22.3.1.740.441
2bjsACVIsopenicillin N synthase1.21.3.10.441
2c3lIDZSerine/threonine-protein kinase Chk12.7.11.10.441
2fzjDH3Dihydrofolate reductase1.5.1.30.441
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
2of2547Tyrosine-protein kinase Lck2.7.10.20.441
2zb1GK4Mitogen-activated protein kinase 14/0.441
3d7zGK5Mitogen-activated protein kinase 14/0.441
3fhxPLPPyridoxal kinase2.7.1.350.441
3tubFPUTyrosine-protein kinase SYK2.7.10.20.441
3vev0H4Glucokinase2.7.1.20.441
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.441
4ftiH7KSerine/threonine-protein kinase Chk12.7.11.10.441
4jbtASDCytochrome P450 monooxygenase/0.441
4qmnDB8Serine/threonine-protein kinase 242.7.11.10.441
9mhtSAHModification methylase HhaI2.1.1.370.441
3rfmCFFAdenosine receptor A2a/0.441
1m9k7NINitric oxide synthase, endothelial1.14.13.390.440
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.440
1qiwDPDCalmodulin/0.440
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2dw4FADLysine-specific histone demethylase 1A10.440
2ed3SAHDiphthine synthase/0.440
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.440
2qhxFE1Pteridine reductase 11.5.1.330.440
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.440
2wn6NDPADP-ribosyltransferase enzymatic component/0.440
2xvw9NRSerum albumin/0.440
3dgeADPSensor histidine kinase/0.440
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.440
3jqgAX6Pteridine reductase, putative/0.440
3nga3NGCasein kinase II subunit alpha2.7.11.10.440
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.440
3qri919Tyrosine-protein kinase ABL12.7.10.20.440
4cdmFO1Deoxyribodipyrimidine photolyase/0.440
4ftu7HKSerine/threonine-protein kinase Chk12.7.11.10.440
4gk3L87Ephrin type-A receptor 32.7.10.10.440