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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2e95B75Geranylgeranyl pyrophosphate synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2e95B75Geranylgeranyl pyrophosphate synthase/1.000
2e94364Geranylgeranyl pyrophosphate synthase/0.585
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.514
2vkeTACTetracycline repressor protein class D/0.488
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.486
3q43D66M1 family aminopeptidase3.4.110.484
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.482
5irnADPNucleotide binding oligomerization domain containing 2/0.478
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.476
3tfn2CJDehydrosqualene synthase/0.474
4b1rITCTetracycline repressor protein class D/0.472
1wuuANPGalactokinase2.7.1.60.471
3vf60H6Glucokinase2.7.1.20.471
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.466
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.466
5dozNDPJamJ/0.464
1re9DSOCamphor 5-monooxygenase1.14.15.10.463
1z6tADPApoptotic protease-activating factor 1/0.461
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.460
3csoXNIGenome polyprotein2.7.7.480.460
2ignFADPyranose 2-oxidase/0.459
2po3T4K4-dehydrase/0.459
4ef9FMNDihydroorotate dehydrogenase (fumarate)/0.457
4iwv1J9Glucokinase2.7.1.20.457
2e20B4PPropionate kinase/0.456
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.454
8catNDPCatalase1.11.1.60.454
3b04OOPIsopentenyl-diphosphate delta-isomerase/0.452
3uklFADUDP-galactopyranose mutase/0.452
4bfsZVSPantothenate kinase2.7.1.330.452
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.452
2zevB71Geranylgeranyl pyrophosphate synthase/0.451
1dfoFFOSerine hydroxymethyltransferase2.1.2.10.450
2x0eTYDWsaF/0.450
2x9dITCTetracycline repressor protein class D/0.450
4h6pFMNChromate reductase/0.450
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.449
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.448
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.448
5dp2NAPCurF/0.448
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
2yltFADPhenylacetone monooxygenase1.14.13.920.447
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.447
4nieNBHNuclear receptor ROR-gamma/0.447
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.447
1x1bSAHC-20 methyltransferase/0.446
2ylrNAPPhenylacetone monooxygenase1.14.13.920.446
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.446
4dhyS41Glucokinase2.7.1.20.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.445
3sf6FDAGlutaryl-CoA dehydrogenase/0.445
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.445
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1kquBR4Phospholipase A2, membrane associated/0.444
1t4u81AProthrombin3.4.21.50.444
2gesCOKPantothenate kinase2.7.1.330.444
3nbvANPKetohexokinase/0.444
3q44D50M1 family aminopeptidase3.4.110.444
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.444
3uwlFOZThymidylate synthase/0.444
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.444
4bb3KKAIsopenicillin N synthase1.21.3.10.443
4p53NAI2-epi-5-epi-valiolone synthase/0.443
3f1kNAPUncharacterized oxidoreductase YciK10.442
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.442
4dpi0N1Beta-secretase 13.4.23.460.442
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.442
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.442
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.441
1pqc444Oxysterols receptor LXR-beta/0.441
1tysDHFThymidylate synthase/0.441
2aclL05Oxysterols receptor LXR-alpha/0.441
2g8yNADHydroxycarboxylate dehydrogenase B/0.441
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
3imxB84Glucokinase2.7.1.20.441
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.441
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.441
2d29FADAcyl-CoA dehydrogenase/0.440
2gv8FADThiol-specific monooxygenase1.14.130.440
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.440
4b2gV1NUncharacterized protein/0.440
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.440
4bfxZVXPantothenate kinase2.7.1.330.440
4fxfATPPyruvate kinase PKM2.7.1.400.440
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.440
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.440
4tm0NAPKtzI/0.440
4xnw2IDP2Y purinoceptor 1/0.440