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
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.11.000
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.695
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.685
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.629
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.606
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.593
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.571
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.557
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.555
2owb626Serine/threonine-protein kinase PLK12.7.11.210.545
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.535
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.521
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.520
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.506
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.497
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.497
2z2w770Wee1-like protein kinase2.7.10.20.494
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.494
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.493
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.491
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.489
5dp2NAPCurF/0.488
3tubFPUTyrosine-protein kinase SYK2.7.10.20.486
3qm4PN0Cytochrome P450 2D6/0.484
1t57FMNConserved protein/0.480
3ctj320Hepatocyte growth factor receptor2.7.10.10.478
3l6jZ90Alr2278 protein/0.477
4g1nNZTPyruvate kinase PKM2.7.1.400.476
4k9yK9YFocal adhesion kinase 12.7.10.20.476
2in6839Wee1-like protein kinase2.7.10.20.474
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.474
1x8b824Wee1-like protein kinase2.7.10.20.472
3n0hTOPDihydrofolate reductase1.5.1.30.470
1s7gNADNAD-dependent protein deacylase 2/0.468
1yc2NADNAD-dependent protein deacylase 2/0.468
2yac937Serine/threonine-protein kinase PLK12.7.11.210.468
1dr5NAPDihydrofolate reductase1.5.1.30.465
2vd0D27Hematopoietic prostaglandin D synthase/0.464
3njoPYVAbscisic acid receptor PYR1/0.464
4h3j10WBeta-secretase 13.4.23.460.464
4bfuZVUPantothenate kinase2.7.1.330.463
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.463
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
4q15HFGProline--tRNA ligase6.1.1.150.462
1s3uTQDDihydrofolate reductase1.5.1.30.461
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.461
3cth319Hepatocyte growth factor receptor2.7.10.10.461
4fnyI3KALK tyrosine kinase receptor2.7.10.10.461
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.461
1c7oPPGHemolysin/0.460
4iaq2GM5-hydroxytryptamine receptor 1B/0.460
4r20AERCytochrome P450 family 17 polypeptide 2/0.460
1d3pBT3Prothrombin3.4.21.50.459
4eevL1XHepatocyte growth factor receptor2.7.10.10.459
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.459
4xq9NADHomospermidine synthase2.5.1.440.459
3gcq1BUMitogen-activated protein kinase 14/0.458
3lfeZ84Mitogen-activated protein kinase 14/0.458
3up3XCAaceDAF-12/0.458
1pd9CO4Dihydrofolate reductase1.5.1.30.457
1disBDMDihydrofolate reductase1.5.1.30.456
1xddAAYIntegrin alpha-L/0.456
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.456
2j0vGDPRac-like GTP-binding protein ARAC7/0.456
3fhxPLPPyridoxal kinase2.7.1.350.456
1yhjR6CPyridoxal kinase2.7.1.350.455
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.455
1hfqMOTDihydrofolate reductase1.5.1.30.454
2ed3SAHDiphthine synthase/0.454
3bi6396Wee1-like protein kinase2.7.10.20.454
2jn3JN3Fatty acid-binding protein, liver/0.453
4h1e10JBeta-secretase 13.4.23.460.453
5k2aZMAAdenosine receptor A2a/0.453
3biz61EWee1-like protein kinase2.7.10.20.452
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.451
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.451
2xviFADPutative flavin-containing monooxygenase/0.451
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
1blzACVIsopenicillin N synthase1.21.3.10.450
1qoqIGPTryptophan synthase alpha chain/0.450
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.450
3aezGDPPantothenate kinase2.7.1.330.450
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3q0gBCOProbable enoyl-CoA hydratase echA84.2.1.170.450
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.450
3fsjD7KBenzoylformate decarboxylase4.1.1.70.449
4lrrCF9Thymidylate synthase/0.449
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1pkfEPDEpothilone C/D epoxidase1.140.448
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3gieACPSensor histidine kinase DesK2.7.13.30.448
3vtdTKDVitamin D3 receptor/0.448
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.448
4xbfFADLysine-specific histone demethylase 1A10.448
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.447
3nga3NGCasein kinase II subunit alpha2.7.11.10.447
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.447
1h35R01Squalene--hopene cyclase4.2.1.1290.446
2wbaFADTrypanothione reductase1.8.1.120.446
5uviZMAAdenosine receptor A2a/0.446
3emlZMAAdenosine receptor A2a/0.446
1mvsDTMDihydrofolate reductase1.5.1.30.445
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.445
2ejzSAHDiphthine synthase/0.445
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.445
3s3vTOPDihydrofolate reductase1.5.1.30.445
3srrQ20Dihydrofolate reductase1.5.1.30.445
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.445
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.445
4kbn25UDihydrofolate reductase1.5.1.30.445
1dhfFOLDihydrofolate reductase1.5.1.30.444
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.444
4bfzZVZPantothenate kinase2.7.1.330.444
1q5dEPBEpothilone C/D epoxidase1.140.443
2y6fM9FIsopenicillin N synthase1.21.3.10.443
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.443
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.443
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.443
4equG6ISerine/threonine-protein kinase 102.7.11.10.443
4tyj0LIFibroblast growth factor receptor 42.7.10.10.443
5k2bZMAAdenosine receptor A2a/0.443
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.442
3fhxPXLPyridoxal kinase2.7.1.350.442
3fznD7KBenzoylformate decarboxylase4.1.1.70.442
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3fnu006HAP protein/0.441
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.441
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.441
3zoiM2WIsopenicillin N synthase1.21.3.10.441
1cm0COAHistone acetyltransferase KAT2B2.3.1.480.440
1yplRA8Prothrombin3.4.21.50.440
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.440
4fhd0TTSpore photoproduct lyase/0.440
4lb2DM5Serum albumin/0.440
5cc9DDFDihydrofolate reductase1.5.1.30.440