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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
4ga34GAFarnesyl pyrophosphate synthase2.5.1.10

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4ga34GAFarnesyl pyrophosphate synthase2.5.1.101.000
4h5dYS4Farnesyl pyrophosphate synthase2.5.1.100.650
4h5cYS4Farnesyl pyrophosphate synthase2.5.1.100.632
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.615
4h5eYS4Farnesyl pyrophosphate synthase2.5.1.100.612
4l2xYL2Farnesyl pyrophosphate synthase2.5.1.100.606
4lfvYS4Farnesyl pyrophosphate synthase2.5.1.100.590
3iczPB6Farnesyl pyrophosphate synthase/0.584
4jvj1MVFarnesyl pyrophosphate synthase2.5.1.100.579
1zw5ZOLFarnesyl pyrophosphate synthase2.5.1.100.559
2opmNI9Farnesyl pyrophosphate synthase2.5.1.100.551
3rywK9HFarnesyl pyrophosphate synthase, putative/0.539
4kqsRISFarnesyl pyrophosphate synthase2.5.1.100.523
2opnSUFFarnesyl pyrophosphate synthase2.5.1.100.521
4nkeRISFarnesyl pyrophosphate synthase2.5.1.100.519
3egt722Farnesyl pyrophosphate synthase/0.516
3ez3ZOLFarnesyl pyrophosphate synthase, putative/0.514
3ldwZOLFarnesyl pyrophosphate synthase, putative/0.513
3dyh721Farnesyl pyrophosphate synthase/0.488
3krfDSTGeranyl diphosphate synthase large subunit/0.488
3ll9ADPIsopentenyl phosphate kinase/0.480
3oabDSTGeranyl diphosphate synthase large subunit/0.479
4avlTMPPolymerase acidic protein/0.470
4ytnFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.470
2ekaSAHDiphthine synthase/0.469
1rqjRISFarnesyl diphosphate synthase2.5.1.100.463
3p8zSAHGenome polyprotein2.1.1.560.463
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.459
3pbzF02Endothiapepsin3.4.23.220.459
5iu86DZAdenosine receptor A2a/0.459
1rx8NAPDihydrofolate reductase1.5.1.30.457
3icpNADNAD-dependent epimerase/dehydratase/0.457
3krfIPEGeranyl diphosphate synthase large subunit/0.457
3pi0F91Endothiapepsin3.4.23.220.457
3q8uADPNucleoside diphosphate kinase/0.457
3iocA5DPantothenate synthetase6.3.2.10.456
2ehlSAHDiphthine synthase/0.455
3vqhIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
1jpaANPEphrin type-B receptor 22.7.10.10.454
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.454
2eniSAHDiphthine synthase/0.453
2hvdADPNucleoside diphosphate kinase A2.7.4.60.453
4bftZVTPantothenate kinase2.7.1.330.453
4ea2RWZDehydrosqualene synthase/0.453
4y3jHICEndothiapepsin3.4.23.220.452
4opgFDAConserved Archaeal protein/0.451
4y380A9Endothiapepsin3.4.23.220.450
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.449
2c29NAPDihydroflavonol 4-reductase/0.449
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
4jlm1NNDeoxycytidine kinase2.7.1.740.449
2b4yAPRNAD-dependent protein deacylase sirtuin-5, mitochondrial/0.448
2emuSAHDiphthine synthase/0.448
3t88S0N1,4-dihydroxy-2-naphthoyl-CoA synthase/0.448
4blrUTPNTPase P4/0.448
4l4xNDPAmphI/0.448
4y3qF02Endothiapepsin3.4.23.220.448
4y57F63Endothiapepsin3.4.23.220.448
1gotGDPGuanine nucleotide-binding protein G(t) subunit alpha-1/0.447
1qf5RPLAdenylosuccinate synthetase/0.447
2pciSAHDiphthine synthase/0.447
2webPP4Penicillopepsin-13.4.23.200.447
3fhxPLPPyridoxal kinase2.7.1.350.447
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.446
2ek2SAHDiphthine synthase/0.446
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
4ks7X4ZSerine/threonine-protein kinase PAK 62.7.11.10.446
4oztP1AEcdysone receptor, putative/0.446
5jjsSAHGenome polyprotein/0.446
1njaDCMThymidylate synthase/0.445
1ra8FOLDihydrofolate reductase1.5.1.30.445
3fpzAHZThiamine thiazole synthase/0.445
3i0pNADMalate dehydrogenase, putative/0.445
5esoTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.445
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.444
1tkaN3TTransketolase 12.2.1.10.444
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1di8DTQCyclin-dependent kinase 22.7.11.220.443
2e17SAHDiphthine synthase/0.443
2ek3SAHDiphthine synthase/0.443
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.443
2z4y252Geranylgeranyl pyrophosphate synthase/0.443
3qlsNDPDihydrofolate reductase1.5.1.30.443
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.443
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1vi2NADQuinate/shikimate dehydrogenase/0.442
1w48APCNTPase P4/0.442
2e15SAHDiphthine synthase/0.442
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.442
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.442
2r2gEMFEugenol synthase 11.1.1.3180.442
4bfzZVZPantothenate kinase2.7.1.330.442
4jln18VDeoxycytidine kinase2.7.1.740.442
4mv8ACPBiotin carboxylase6.3.4.140.442
4yd7F5NEndothiapepsin3.4.23.220.442
1t57FMNConserved protein/0.441
1txtCAAHMG-CoA synthase/0.441
2p6dSAHDiphthine synthase/0.441
4a862ANMajor pollen allergen Bet v 1-A/0.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4kqsIPEFarnesyl pyrophosphate synthase2.5.1.100.441
4lx9ACON-alpha-acetyltransferase2.3.10.441
4uckSAMLarge structural protein/0.441
2owkSAHDiphthine synthase/0.440
2pckSAHDiphthine synthase/0.440
2y0mACOHistone acetyltransferase KAT8/0.440
3nd6ATPPhosphopantetheine adenylyltransferase/0.440
3pwwROCEndothiapepsin3.4.23.220.440
4k6mSAHGenome polyprotein/0.440
4l5b1UXDeoxycytidine kinase2.7.1.740.440
4opiFDAConserved Archaeal protein/0.440
5iqiGNPBifunctional AAC/APH2.3.10.440