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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
3k3bL31Kinesin-like protein KIF11

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3k3bL31Kinesin-like protein KIF11/1.000
2x7dEGBKinesin-like protein KIF11/0.639
1q0bNATKinesin-like protein KIF11/0.633
2iehMOYKinesin-like protein KIF11/0.614
2q2zMKKKinesin-like protein KIF11/0.613
3k5eK5EKinesin-like protein KIF11/0.611
4bbgV02Kinesin-like protein KIF11/0.610
1x88NATKinesin-like protein KIF11/0.603
2x7eX7EKinesin-like protein KIF11/0.590
3kenZZDKinesin-like protein KIF11/0.581
2wogZZDKinesin-like protein KIF11/0.580
2x2rX2OKinesin-like protein KIF11/0.567
2xae2XAKinesin-like protein KIF11/0.567
2fme3QCKinesin-like protein KIF11/0.547
4a51DQ8Kinesin-like protein KIF11/0.538
2gm12AZKinesin-like protein KIF11/0.505
4as76LXKinesin-like protein KIF11/0.505
4a5yG7XKinesin-like protein KIF11/0.495
4z34ON7Lysophosphatidic acid receptor 1/0.491
1w2xRCPAcetyl-CoA carboxylase/0.487
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.481
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.479
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.478
2itpAEEEpidermal growth factor receptor2.7.10.10.476
1h1pCMGCyclin-dependent kinase 22.7.11.220.475
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.475
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.475
3bgqVX2Serine/threonine-protein kinase pim-12.7.11.10.471
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.469
4erwSTUCyclin-dependent kinase 22.7.11.220.469
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.468
3unk0BYCyclin-dependent kinase 22.7.11.220.467
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.464
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.463
2ydiYDISerine/threonine-protein kinase Chk12.7.11.10.463
2wpa889Cyclin-dependent kinase 22.7.11.220.461
4bdhWVISerine/threonine-protein kinase Chk22.7.11.10.461
4fswHK6Serine/threonine-protein kinase Chk12.7.11.10.460
4k181OBSerine/threonine-protein kinase pim-12.7.11.10.460
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.460
4zvmDM2Ribosyldihydronicotinamide dehydrogenase [quinone]/0.460
5jr34MUCarminomycin 4-O-methyltransferase DnrK2.1.1.2920.460
1h1s4SPCyclin-dependent kinase 22.7.11.220.459
3flsFLSMitogen-activated protein kinase 14/0.459
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.458
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
3r73X87Cyclin-dependent kinase 22.7.11.220.458
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
2nr4FMNConserved protein/0.457
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.457
3orzBI43-phosphoinositide-dependent protein kinase 12.7.11.10.457
3qu0X40Cyclin-dependent kinase 22.7.11.220.457
4hyh1AMSerine/threonine-protein kinase Chk12.7.11.10.457
1ckpPVBCyclin-dependent kinase 22.7.11.220.456
2c3lIDZSerine/threonine-protein kinase Chk12.7.11.10.456
2e9oA58Serine/threonine-protein kinase Chk12.7.11.10.456
2y9qANPMitogen-activated protein kinase 12.7.11.240.456
1qnfFADDeoxyribodipyrimidine photo-lyase4.1.99.30.455
1uvrBI83-phosphoinositide-dependent protein kinase 12.7.11.10.455
1vyw292Cyclin-dependent kinase 22.7.11.220.455
2brhDFWSerine/threonine-protein kinase Chk12.7.11.10.455
2wtcVGMSerine/threonine-protein kinase Chk22.7.11.10.455
2x1nX1NCyclin-dependent kinase 22.7.11.220.455
4fsyHK7Serine/threonine-protein kinase Chk12.7.11.10.455
1fvt106Cyclin-dependent kinase 22.7.11.220.454
4bcpT3CCyclin-dependent kinase 22.7.11.220.454
4ek610KCyclin-dependent kinase 22.7.11.220.454
4ftu7HKSerine/threonine-protein kinase Chk12.7.11.10.454
4m37SAHProtein arginine N-methyltransferase 72.1.10.454
1iepSTITyrosine-protein kinase ABL12.7.10.20.453
1oi9N20Cyclin-dependent kinase 22.7.11.220.453
4ddrMMVDihydrofolate reductase1.5.1.30.453
4eor4SPCyclin-dependent kinase 22.7.11.220.453
4h7zGUNQueuine tRNA-ribosyltransferase2.4.2.290.453
3bhtMFRCyclin-dependent kinase 22.7.11.220.452
3o0g3O0Cyclin-dependent-like kinase 52.7.11.10.452
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
2qmzLDPRibosyldihydronicotinamide dehydrogenase [quinone]/0.451
2uzlC94Cyclin-dependent kinase 22.7.11.220.451
3nuuJOZ3-phosphoinositide-dependent protein kinase 12.7.11.10.451
1fwkADPHomoserine kinase2.7.1.390.450
2hog710Serine/threonine-protein kinase Chk12.7.11.10.450
3c4eC4ESerine/threonine-protein kinase pim-12.7.11.10.450
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.450
3qcs3Q13-phosphoinositide-dependent protein kinase 12.7.11.10.450
4gg70J8Hepatocyte growth factor receptor2.7.10.10.450
4yqfGDPSeptin-9/0.450
1dm2HMDCyclin-dependent kinase 22.7.11.220.449
1f20FADNitric oxide synthase, brain1.14.13.390.449
1phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.449
4qysPLRTryptophan synthase beta chain 24.2.1.200.449
2brmDFZSerine/threonine-protein kinase Chk12.7.11.10.448
2hxq373Serine/threonine-protein kinase Chk12.7.11.10.448
2tsrD16Thymidylate synthase2.1.1.450.448
3zt0ZT0Integrase/0.448
4u9aSTUInterleukin-1 receptor-associated kinase 42.7.11.10.448
1svlADPLarge T antigen3.6.40.447
1ykdCMPAdenylate cyclase/0.447
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.447
2ptfFMNUncharacterized protein MTH_863/0.447
3ujlA8SAbscisic acid receptor PYL2/0.447
4fmqANPMitogen-activated protein kinase 12.7.11.240.447
1mc1PCXCarboxyethyl-arginine beta-lactam-synthase6.3.3.40.446
1rc4DDFDihydrofolate reductase1.5.1.30.446
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.446
4eomATPCyclin-dependent kinase 22.7.11.220.446
4ft5H2KSerine/threonine-protein kinase Chk12.7.11.10.446
4gcmNAPThioredoxin reductase1.8.1.90.446
1rx4DDFDihydrofolate reductase1.5.1.30.445
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.445
3qtqX35Cyclin-dependent kinase 22.7.11.220.445
3rni21ZCyclin-dependent kinase 22.7.11.220.445
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.445
4fszHK8Serine/threonine-protein kinase Chk12.7.11.10.445
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
1mk1APRMutT/nudix family protein/0.444
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.444
2iw84SPCyclin-dependent kinase 22.7.11.220.444
3gi3B10Mitogen-activated protein kinase 14/0.444
3qj0QI3Botulinum neurotoxin type A3.4.24.690.444
3qqlX03Cyclin-dependent kinase 22.7.11.220.444
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.444
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4ftaH5KSerine/threonine-protein kinase Chk12.7.11.10.444
5il2SAHN6-adenosine-methyltransferase 70 kDa subunit/0.444
2hy0306Serine/threonine-protein kinase Chk12.7.11.10.443
3ox1695Ribosyldihydronicotinamide dehydrogenase [quinone]/0.443
4anqVGHALK tyrosine kinase receptor2.7.10.10.443
4ez30S0Cyclin-dependent kinase 22.7.11.220.443
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.443
1uu7BI23-phosphoinositide-dependent protein kinase 12.7.11.10.442
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
2qkrIXMCdc2-like CDK2/CDC28 like protein kinase/0.442
2wmuZYUSerine/threonine-protein kinase Chk12.7.11.10.442
2wtdZZKSerine/threonine-protein kinase Chk22.7.11.10.442
3a4pDFQHepatocyte growth factor receptor2.7.10.10.442
4ftcH6KSerine/threonine-protein kinase Chk12.7.11.10.442
4ww9ADPEKC/KEOPS complex subunit BUD323.60.442
2zazGK1Mitogen-activated protein kinase 14/0.441
3ggj25HHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.441
3s0o50ZCyclin-dependent kinase 22.7.11.220.441
3s4qNK0Mitogen-activated protein kinase 14/0.441
3tiz3TICyclin-dependent kinase 22.7.11.220.441
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.441
1qiwDPDCalmodulin/0.440
1zys199Serine/threonine-protein kinase Chk12.7.11.10.440
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.440
2br1PFPSerine/threonine-protein kinase Chk12.7.11.10.440
3ddqRRCCyclin-dependent kinase 22.7.11.220.440
3q0gBCOProbable enoyl-CoA hydratase echA84.2.1.170.440
3s00Z60Cyclin-dependent kinase 22.7.11.220.440
3tkh07SSerine/threonine-protein kinase Chk12.7.11.10.440
3vt7VDXVitamin D3 receptor/0.440
4c02TAKActivin receptor type-12.7.11.300.440
4lg5A1OAbscisic acid receptor PYL2/0.440
4wboANWRhodopsin kinase/0.440