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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
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.11.000
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.594
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.591
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.586
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.582
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.582
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.576
2z2w770Wee1-like protein kinase2.7.10.20.575
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.573
2in6839Wee1-like protein kinase2.7.10.20.555
2yac937Serine/threonine-protein kinase PLK12.7.11.210.555
2owb626Serine/threonine-protein kinase PLK12.7.11.210.551
1x8b824Wee1-like protein kinase2.7.10.20.541
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.533
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.522
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.522
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.521
2io6330Wee1-like protein kinase2.7.10.20.520
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.520
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.519
3biz61EWee1-like protein kinase2.7.10.20.519
3cr0809Wee1-like protein kinase2.7.10.20.518
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.508
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.507
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.502
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.502
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.499
3bi6396Wee1-like protein kinase2.7.10.20.495
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.486
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.485
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.484
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.481
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.478
3cqeP91Wee1-like protein kinase2.7.10.20.478
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.477
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.475
2ejzSAHDiphthine synthase/0.473
1t57FMNConserved protein/0.472
2vetUMPThymidylate synthase/0.466
3h1vTK1Glucokinase2.7.1.20.464
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.463
2ed3SAHDiphthine synthase/0.463
1qoqIGPTryptophan synthase alpha chain/0.462
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4twnB96Ephrin type-A receptor 32.7.10.10.462
2zevB71Geranylgeranyl pyrophosphate synthase/0.457
3c1oNAPEugenol synthase/0.457
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
1yc2NADNAD-dependent protein deacylase 2/0.456
4bfuZVUPantothenate kinase2.7.1.330.456
5dp2NAPCurF/0.456
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.455
1g63FMNEpidermin decarboxylase4.1.10.452
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2gjlFMNNitronate monooxygenase1.13.12.160.452
3njoPYVAbscisic acid receptor PYR1/0.450
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.450
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.450
4f3gKAIGlutamate receptor 3/0.449
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
5bn3ADPV-type ATP synthase alpha chain/0.448
5bn3ADPNEQ263/0.448
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.447
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.447
2gq3COAMalate synthase G/0.447
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.447
1cqp803Integrin alpha-L/0.446
1dr3TAPDihydrofolate reductase1.5.1.30.446
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.446
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.446
1xddAAYIntegrin alpha-L/0.445
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.445
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.445
4djw0KPBeta-secretase 13.4.23.460.445
2xvw9NRSerum albumin/0.444
3c35KAIGlutamate receptor ionotropic, kainate 1/0.444
4bfvZVVPantothenate kinase2.7.1.330.444
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.444
2uxhQUEHTH-type transcriptional regulator TtgR/0.443
4at0FADPossible succinate dehydrogenase/0.443
1s3uTQDDihydrofolate reductase1.5.1.30.442
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.442
2cleF6FTryptophan synthase alpha chain/0.442
2uxoTACHTH-type transcriptional regulator TtgR/0.442
3af0GDPPantothenate kinase2.7.1.330.442
3fhxPLPPyridoxal kinase2.7.1.350.442
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.442
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.441
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.441
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
5k2cZMAAdenosine receptor A2a/0.441
5k2aZMAAdenosine receptor A2a/0.441
2a94AP0L-lactate dehydrogenase1.1.1.270.440
2w6cBM4Acetylcholinesterase3.1.1.70.440
2xvv9DNSerum albumin/0.440
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4fsyHK7Serine/threonine-protein kinase Chk12.7.11.10.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.440
5iu86DZAdenosine receptor A2a/0.440