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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
3plsANPMacrophage-stimulating protein receptor2.7.10.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3plsANPMacrophage-stimulating protein receptor2.7.10.11.000
3p23ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.553
1qcfPP1Tyrosine-protein kinase HCK2.7.10.20.540
1b38ATPCyclin-dependent kinase 22.7.11.220.526
4fl3ANPTyrosine-protein kinase SYK2.7.10.20.524
1b39ATPCyclin-dependent kinase 22.7.11.220.521
2h8hH8HProto-oncogene tyrosine-protein kinase Src2.7.10.20.519
3vs3VSETyrosine-protein kinase HCK2.7.10.20.511
1qmzATPCyclin-dependent kinase 22.7.11.220.510
4k2rANPTyrosine-protein kinase ZAP-702.7.10.20.507
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.506
4fl2ANPTyrosine-protein kinase SYK2.7.10.20.504
1hckATPCyclin-dependent kinase 22.7.11.220.502
2ozoANPTyrosine-protein kinase ZAP-702.7.10.20.501
1j1cADPGlycogen synthase kinase-3 beta2.7.11.260.496
2wouZZFTGF-beta receptor type-12.7.11.300.496
4riyANPReceptor tyrosine-protein kinase erbB-32.7.10.10.496
4qnyANPMitogen activated protein kinase, putative/0.494
2cjmATPCyclin-dependent kinase 22.7.11.220.493
4k8aK8AFocal adhesion kinase 12.7.10.20.492
3lmgANPReceptor tyrosine-protein kinase erbB-32.7.10.10.491
1jstATPCyclin-dependent kinase 22.7.11.220.488
3vs0VS0Tyrosine-protein kinase HCK2.7.10.20.488
1i44ACPInsulin receptor2.7.10.10.487
4m69ANPReceptor-interacting serine/threonine-protein kinase 32.7.11.10.487
3w33W19Epidermal growth factor receptor2.7.10.10.486
4ysjADPCalmodulin-like domain protein kinase/0.486
1dayGNPCasein kinase II subunit alpha2.7.11.10.483
3c4wATPRhodopsin kinase/0.483
3my5RFZCyclin-dependent kinase 22.7.11.220.483
5cnnANPEpidermal growth factor receptor2.7.10.10.483
5c03AGSNon-receptor tyrosine-protein kinase TYK22.7.10.20.481
1pxoCK7Cyclin-dependent kinase 22.7.11.220.480
1w8cN69Cyclin-dependent kinase 22.7.11.220.480
2btsU32Cyclin-dependent kinase 22.7.11.220.479
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.478
3q4zANPSerine/threonine-protein kinase PAK 12.7.11.10.478
1mruAGSSerine/threonine-protein kinase PknB2.7.11.10.477
3cokANPSerine/threonine-protein kinase PLK42.7.11.210.477
1ad5ANPTyrosine-protein kinase HCK2.7.10.20.476
3vs5VSGTyrosine-protein kinase HCK2.7.10.20.476
4jrnANPRhoptry kinase family protein/0.475
4lrjANPUncharacterized protein/0.475
2c5yMTWCyclin-dependent kinase 22.7.11.220.474
4bcmT7ZCyclin-dependent kinase 22.7.11.220.474
4i3zADPCyclin-dependent kinase 22.7.11.220.474
4qmlANPSerine/threonine-protein kinase 242.7.11.10.474
3qc9ADPRhodopsin kinase/0.473
3vs2VSBTyrosine-protein kinase HCK2.7.10.20.472
2btrU73Cyclin-dependent kinase 22.7.11.220.471
1ictT44Transthyretin/0.469
4k33ACPFibroblast growth factor receptor 32.7.10.10.469
3c4zADPRhodopsin kinase/0.468
1finATPCyclin-dependent kinase 22.7.11.220.467
3fzpAGSProtein-tyrosine kinase 2-beta2.7.10.20.467
2vtqLZACyclin-dependent kinase 22.7.11.220.466
2w4jADPDeath-associated protein kinase 12.7.11.10.466
4ii5ADPCyclin-dependent kinase 22.7.11.220.466
5eg3ACPFibroblast growth factor receptor 2/0.466
3ztxZTXAurora kinase B-A2.7.11.10.465
2c6o4SPCyclin-dependent kinase 22.7.11.220.464
2ym6YM6Serine/threonine-protein kinase Chk12.7.11.10.464
3bu5ATPInsulin receptor2.7.10.10.464
3orpAGSSerine/threonine protein kinase/0.464
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.464
2wotZZGTGF-beta receptor type-12.7.11.300.463
1ie4T44Transthyretin/0.462
2henADPEphrin type-B receptor 22.7.10.10.462
3nux3NVCyclin-dependent kinase 62.7.11.220.462
4y12AGSSerine/threonine-protein kinase PknG2.7.11.10.462
2csnCKICasein kinase I homolog 12.7.11.10.461
3amaSKEcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.461
3nieANPMitogen-activated protein kinase/0.461
3zonIK1Non-receptor tyrosine-protein kinase TYK22.7.10.20.461
4hni16WCasein kinase I isoform epsilon2.7.11.10.461
2b9fADPMitogen-activated protein kinase FUS32.7.11.240.460
4ez50RSCyclin-dependent kinase 62.7.11.220.460
4pl4ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.460
4xlvACPInsulin receptor2.7.10.10.460
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.459
2vnwM01cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
2y9qANPMitogen-activated protein kinase 12.7.11.240.459
1oitHDTCyclin-dependent kinase 22.7.11.220.458
1d7yFADFerredoxin reductase/0.457
1q5kTMUGlycogen synthase kinase-3 beta2.7.11.260.457
2b9iADPMitogen-activated protein kinase FUS32.7.11.240.457
5cnoANPEpidermal growth factor receptor2.7.10.10.457
1gii1PUCyclin-dependent kinase 22.7.11.220.456
4wq5ATPtRNA N6-adenosine threonylcarbamoyltransferase/0.456
1xr1ANPSerine/threonine-protein kinase pim-12.7.11.10.455
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.455
2c6eHPMAurora kinase A2.7.11.10.455
3e8cG96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
3rak03ZCyclin-dependent kinase 22.7.11.220.455
3zh8C58Protein kinase C iota type2.7.11.130.455
4crsAGSSerine/threonine-protein kinase N22.7.11.130.455
4l9i8PRRhodopsin kinase/0.455
1ig1ANPDeath-associated protein kinase 12.7.11.10.454
1jkkANPDeath-associated protein kinase 12.7.11.10.454
2etm7PYFocal adhesion kinase 12.7.10.20.454
2hog710Serine/threonine-protein kinase Chk12.7.11.10.454
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
4fv2EK5Mitogen-activated protein kinase 12.7.11.240.454
2qoqANPEphrin type-A receptor 32.7.10.10.453
3vrzVRZTyrosine-protein kinase HCK2.7.10.20.453
3vs1VSATyrosine-protein kinase HCK2.7.10.20.453
4grb0XGCasein kinase II subunit alpha2.7.11.10.453
4lfiGNPCasein kinase II subunit alpha2.7.11.10.453
5dpvSKEAurora kinase A2.7.11.10.453
1q97ATPSerine/threonine-protein kinase SKY12.7.11.10.452
1zaoATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.452
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.452
3ortAGSSerine/threonine protein kinase/0.452
4eooATPCyclin-dependent kinase 22.7.11.220.452
4fkg4CKCyclin-dependent kinase 22.7.11.220.452
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
1pxlCK4Cyclin-dependent kinase 22.7.11.220.451
1vjy460TGF-beta receptor type-12.7.11.300.451
3ezvEZVCyclin-dependent kinase 22.7.11.220.451
3q9xEMOCasein kinase II subunit alpha2.7.11.10.451
5j23A2RPutative 2-hydroxyacid dehydrogenase/0.451
2b9jADPMitogen-activated protein kinase FUS32.7.11.240.450
3c4xATPRhodopsin kinase/0.450
3rwpABQ3-phosphoinositide-dependent protein kinase 12.7.11.10.450
4ic7ANPMitogen-activated protein kinase 72.7.11.240.450
1o6kANPRAC-beta serine/threonine-protein kinase2.7.11.10.449
2cbsR13Cellular retinoic acid-binding protein 2/0.449
2vtsLZCCyclin-dependent kinase 22.7.11.220.449
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.449
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.449
4rvoADPPhenylacetate-coenzyme A ligase/0.449
3o7lANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3oogYTPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3w32W32Epidermal growth factor receptor2.7.10.10.448
3x2uATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
5ap7SVEDual specificity protein kinase TTK2.7.12.10.448
1ir3ANPInsulin receptor2.7.10.10.447
2ghmLICMitogen-activated protein kinase 14/0.447
3r8lZ30Cyclin-dependent kinase 22.7.11.220.447
3hkoANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands/0.446
3r1yX76Cyclin-dependent kinase 22.7.11.220.446
4bbe3O4Tyrosine-protein kinase JAK2/0.446
4jajXU1Aurora kinase A2.7.11.10.446
5dnrATPAurora kinase A2.7.11.10.446
1e1xNW1Cyclin-dependent kinase 22.7.11.220.445
2j0lANPFocal adhesion kinase 12.7.10.20.445
2vv9IM9Cyclin-dependent kinase 22.7.11.220.445
3vn9ANKDual specificity mitogen-activated protein kinase kinase 62.7.12.20.445
3ea0ATPATPase, ParA family/0.444
3js2VM1Fibroblast growth factor receptor 1/0.444
3keuATPPyridoxal kinase2.7.1.350.444
3tkh07SSerine/threonine-protein kinase Chk12.7.11.10.444
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4xhgADPUncharacterized protein/0.444
4xldBRLPeroxisome proliferator-activated receptor gamma/0.444
1w0xOLOCyclin-dependent kinase 22.7.11.220.443
2ojf4PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
4bi0Z0WDual specificity protein kinase TTK2.7.12.10.443
4fklCK2Cyclin-dependent kinase 22.7.11.220.443
4yhjAN2G protein-coupled receptor kinase 42.7.11.160.443
1f8sFADL-amino-acid oxidase1.4.3.20.442
1ny3ADPMAP kinase-activated protein kinase 22.7.11.10.442
2ijmATPFocal adhesion kinase 12.7.10.20.442
2pvlP55Casein kinase II subunit alpha2.7.11.10.442
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.442
3gu7ADPDeath-associated protein kinase 12.7.11.10.442
3rpo24ZCyclin-dependent kinase 22.7.11.220.442
3s1h56ZCyclin-dependent kinase 22.7.11.220.442
3s2pPMUCyclin-dependent kinase 22.7.11.220.442
4deeADPAurora kinase A2.7.11.10.442
1jqhANPInsulin-like growth factor 1 receptor2.7.10.10.441
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.441
2uzbC75Cyclin-dependent kinase 22.7.11.220.441
3a5mATPMajor actin/0.441
3t80CTN2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.441
4bl1ANPMaternal embryonic leucine zipper kinase2.7.11.10.441
4ekkANPRAC-alpha serine/threonine-protein kinase2.7.11.10.441
4fg9ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.441
4s26SAHPhosphomethylpyrimidine synthase, chloroplastic4.1.99.170.441
1ewyFADFerredoxin--NADP reductase1.18.1.20.440
1g5sI17Cyclin-dependent kinase 22.7.11.220.440
2a0cCK9Cyclin-dependent kinase 22.7.11.220.440
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.440
3nbzGTPGTP-binding nuclear protein Ran/0.440
4c4h7RODual specificity protein kinase TTK2.7.12.10.440
4l7sG7KTyrosine-protein kinase ITK/TSK2.7.10.20.440