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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
4ga34GAFarnesyl pyrophosphate synthase2.5.1.10

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ga34GAFarnesyl pyrophosphate synthase2.5.1.101.000
4h5dYS4Farnesyl pyrophosphate synthase2.5.1.100.650
4h5cYS4Farnesyl pyrophosphate synthase2.5.1.100.625
4h5eYS4Farnesyl pyrophosphate synthase2.5.1.100.612
4lfvYS4Farnesyl pyrophosphate synthase2.5.1.100.610
3iczPB6Farnesyl pyrophosphate synthase/0.604
3rywK9HFarnesyl pyrophosphate synthase, putative/0.596
4l2xYL2Farnesyl pyrophosphate synthase2.5.1.100.591
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.586
4jvj1MVFarnesyl pyrophosphate synthase2.5.1.100.585
3dyh721Farnesyl pyrophosphate synthase/0.567
3egt722Farnesyl pyrophosphate synthase/0.563
2opmNI9Farnesyl pyrophosphate synthase2.5.1.100.554
2f94BFQFarnesyl pyrophosphate synthase2.5.1.100.511
4q23RISFarnesyl pyrophosphate synthase2.5.1.100.504
3gu83GUDeath-associated protein kinase 12.7.11.10.494
3oabDSTGeranyl diphosphate synthase large subunit/0.491
3krfDSTGeranyl diphosphate synthase large subunit/0.490
4opgFDAConserved Archaeal protein/0.490
4nkeRISFarnesyl pyrophosphate synthase2.5.1.100.488
4avlTMPPolymerase acidic protein/0.486
1lcbDHFThymidylate synthase/0.483
1w48APCNTPase P4/0.483
4de50JDPantothenate synthetase6.3.2.10.478
1e81M91Endothiapepsin3.4.23.220.477
4ytnFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.476
4uckSAMLarge structural protein/0.475
5iu86DZAdenosine receptor A2a/0.475
1n2hPAJPantothenate synthetase6.3.2.10.474
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.474
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
4blrUTPNTPase P4/0.473
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.472
3q8uADPNucleoside diphosphate kinase/0.472
3rbmB73Farnesyl pyrophosphate synthase, putative/0.472
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.471
1rp0AHZThiamine thiazole synthase, chloroplastic/0.470
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.469
4dptAGSMevalonate diphosphate decarboxylase/0.469
4hr2ADPNucleoside diphosphate kinase/0.469
4opiFDAConserved Archaeal protein/0.469
2dxfGNPNucleoside diphosphate kinase2.7.4.60.467
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.467
3ivgFG5Pantothenate synthetase6.3.2.10.466
5ftfADPTPR domain protein/0.466
2oz57XYUncharacterized protein/0.464
3ldwZOLFarnesyl pyrophosphate synthase, putative/0.464
3qd03Q43-phosphoinositide-dependent protein kinase 12.7.11.10.464
4y57F63Endothiapepsin3.4.23.220.464
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.463
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.462
3p8zSAHGenome polyprotein2.1.1.560.462
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.460
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.460
5esoISC2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.460
1mv8GDXGDP-mannose 6-dehydrogenase1.1.1.1320.459
2b4yAPRNAD-dependent protein deacylase sirtuin-5, mitochondrial/0.459
3ivxFG6Pantothenate synthetase6.3.2.10.459
4jlm1NNDeoxycytidine kinase2.7.1.740.459
1d8fSPIStromelysin-13.4.24.170.458
2wdzNADGalactitol dehydrogenase/0.458
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.458
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
1lcbTMPThymidylate synthase/0.457
1njaDCMThymidylate synthase/0.457
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.457
3h3r14HCollagen type IV alpha-3-binding protein/0.457
3kb1ADPIron-sulfur cluster carrier protein/0.457
1ve3SAMUncharacterized protein/0.456
1zw5ZOLFarnesyl pyrophosphate synthase2.5.1.100.456
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.456
2i191BYFarnesyl pyrophosphate synthase/0.456
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.456
1gotGDPGuanine nucleotide-binding protein G(t) subunit alpha-1/0.455
1kvkATPMevalonate kinase2.7.1.360.455
1nhkCMPNucleoside diphosphate kinase2.7.4.60.455
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4kqsRISFarnesyl pyrophosphate synthase2.5.1.100.455
4rx6ATPNitrogen regulatory PII-like protein/0.455
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.454
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.454
4dwb0M7Farnesyl pyrophosphate synthase/0.454
4y380A9Endothiapepsin3.4.23.220.454
5c3jFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.454
5jjsSAHGenome polyprotein/0.454
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.453
1svmATPLarge T antigen3.6.40.453
3k2xI5A2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.453
3lzs017Gag-Pol polyprotein3.4.23.160.453
3nd6ATPPhosphopantetheine adenylyltransferase/0.453
5iubCLRAdenosine receptor A2a/0.453
2ifaFMNUncharacterized protein/0.452
3rpy27ZCyclin-dependent kinase 22.7.11.220.452
5djtFMNNPH1-2/0.452
5f8fSFGPossible transcriptional regulatory protein/0.452
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.451
1rqjRISFarnesyl diphosphate synthase2.5.1.100.451
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.451
3bsc2PDGenome polyprotein2.7.7.480.451
3bwcSAMSpermidine synthase, putative/0.451
3gbuATPUncharacterized sugar kinase PH14592.7.10.451
4dfg0JVGag-Pol polyprotein3.4.23.160.451
5djuFMNNPH1-2/0.451
1gky5GPGuanylate kinase2.7.4.80.450
1m17AQ4Epidermal growth factor receptor2.7.10.10.450
2ayp43ASerine/threonine-protein kinase Chk12.7.11.10.450
2zevIPEGeranylgeranyl pyrophosphate synthase/0.450
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.450
3iocA5DPantothenate synthetase6.3.2.10.450
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.450
4bdhWVISerine/threonine-protein kinase Chk22.7.11.10.450
4bk3FADProbable salicylate monooxygenase/0.450
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4jln18VDeoxycytidine kinase2.7.1.740.450
1dr3TAPDihydrofolate reductase1.5.1.30.449
2givACOHistone acetyltransferase KAT8/0.449
3ac3KSHTyrosine-protein kinase Lck2.7.10.20.449
3isjA8DPantothenate synthetase6.3.2.10.449
3qcx3Q23-phosphoinositide-dependent protein kinase 12.7.11.10.449
3toxNAPPutative oxidoreductase/0.449
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.449
4nmbFADBifunctional protein PutA/0.449
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
1kp3ATPArgininosuccinate synthase6.3.4.50.448
2dxdANPNucleoside diphosphate kinase2.7.4.60.448
2geuCOKPantothenate kinase2.7.1.330.448
2jt2C90UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.448
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
3pbzF02Endothiapepsin3.4.23.220.448
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.448
4lx9ACON-alpha-acetyltransferase2.3.10.448
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.448
1di8DTQCyclin-dependent kinase 22.7.11.220.447
2c29NAPDihydroflavonol 4-reductase/0.447
2hveADPNucleoside diphosphate kinase A2.7.4.60.447
2izfBTNStreptavidin/0.447
3clsFADElectron transfer flavoprotein subunit alpha/0.447
3fx6BPXCarboxypeptidase A13.4.17.10.447
4jldADPAdenylate kinase/0.447
4rpgFADUDP-galactopyranose mutase5.4.99.90.447
4rvgTYDD-mycarose 3-C-methyltransferase/0.447
4u03GTPCyclic GMP-AMP synthase/0.447
1af7SAHChemotaxis protein methyltransferase2.1.1.800.446
1d6w00RProthrombin3.4.21.50.446
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.446
2g89UMPThymidylate synthase/0.446
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.446
2p41SAHGenome polyprotein/0.446
3e2sFADBifunctional protein PutA1.5.5.20.446
3eluSAMMethyltransferase/0.446
3iodA6DPantothenate synthetase6.3.2.10.446
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.446
3psyRB9Endothiapepsin3.4.23.220.446
3pwwROCEndothiapepsin3.4.23.220.446
3tneRITCandidapepsin-13.4.23.240.446
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1ia1NDPDihydrofolate reductase1.5.1.30.445
1pgtGTXGlutathione S-transferase P2.5.1.180.445
1rwbNADGlucose 1-dehydrogenase1.1.1.470.445
1sxjAGSReplication factor C subunit 1/0.445
1txtCAAHMG-CoA synthase/0.445
2jahNDPClavaldehyde dehydrogenase/0.445
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.445
3bj7COADiamine acetyltransferase 1/0.445
3coy53HPantothenate synthetase6.3.2.10.445
3rn8RN8Glutamate receptor 2/0.445
4d0lGSPRas-related protein Rab-11A/0.445
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.445
4ftaH5KSerine/threonine-protein kinase Chk12.7.11.10.445
5kj6NAJAlcohol dehydrogenase E chain1.1.1.10.445
1nueGDPNucleoside diphosphate kinase B2.7.4.60.444
1r5gAO1Methionine aminopeptidase 2/0.444
1szfFMNCytochrome b2, mitochondrial1.1.2.30.444
2b1i93ABifunctional purine biosynthesis protein PURH2.1.2.30.444
2r6gATPMaltose/maltodextrin import ATP-binding protein MalK/0.444
3clrFADElectron transfer flavoprotein subunit alpha/0.444
3imeBZ2Pantothenate synthetase6.3.2.10.444
3lqfNADGalactitol dehydrogenase/0.444
3unk0BYCyclin-dependent kinase 22.7.11.220.444
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.444
4kc2WS2Histo-blood group ABO system transferase/0.444
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.444
4s1iPLPPyridoxal kinase, putative/0.444
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.444
5epeSAHUncharacterized protein/0.444
1h60STRPentaerythritol tetranitrate reductase/0.443
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.443
1tj1FADBifunctional protein PutA1.5.5.20.443
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.443
2fznFADBifunctional protein PutA1.5.5.20.443
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.443
2gr2APRFerredoxin reductase/0.443
2webPP4Penicillopepsin-13.4.23.200.443
2zrjAGSProtein RecA/0.443
3a3gDLZLumazine protein/0.443
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.443
3fhxPXLPyridoxal kinase2.7.1.350.443
3imgBZ2Pantothenate synthetase6.3.2.10.443
3ioeA7DPantothenate synthetase6.3.2.10.443
3ldoANP78 kDa glucose-regulated protein/0.443
3mp5HMGHydroxymethylglutaryl-CoA lyase, mitochondrial4.1.3.40.443
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.443
4j7xNAPSepiapterin reductase1.1.1.1530.443
4k6mSAHGenome polyprotein/0.443
4o1mNADEnoyl-acyl carrier reductase/0.443
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
5ccyTMPPolymerase acidic protein/0.443
5hg0SAMPantothenate synthetase/0.443
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.442
1knpFADL-aspartate oxidase1.4.3.160.442
1kqcFMNOxygen-insensitive NAD(P)H nitroreductase/0.442
1qf4RPDAdenylosuccinate synthetase/0.442
1t57FMNConserved protein/0.442
2ylzFADPhenylacetone monooxygenase1.14.13.920.442
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.442
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3eksCY9Actin-5C/0.442
3evcSAHGenome polyprotein2.1.1.560.442
3mtfA3FActivin receptor type-12.7.11.300.442
3ohoZ79Stromelysin-13.4.24.170.442
3qtxX43Cyclin-dependent kinase 22.7.11.220.442
3qzhX69Cyclin-dependent kinase 22.7.11.220.442
3rak03ZCyclin-dependent kinase 22.7.11.220.442
3zxzKRWHepatocyte growth factor receptor2.7.10.10.442
4au8Z3RCyclin-dependent-like kinase 52.7.11.10.442
4blsAPCNTPase P4/0.442
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.442
4opuFDAConserved Archaeal protein/0.442
4ww0ADPATP-dependent zinc metalloprotease FtsH/0.442
4zeaIMIEndothiapepsin3.4.23.220.442
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.442
1dgmADNAdenosine kinase2.7.1.200.441
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1dssNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.441
1feaFADTrypanothione reductase1.8.1.120.441
1hbvGANGag-Pol polyprotein/0.441
1jmhUMPThymidylate synthase/0.441
1qo8FADFumarate reductase flavoprotein subunit/0.441
1scuCOASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.441
1t2aNDPGDP-mannose 4,6 dehydratase4.2.1.470.441
1tj2FADBifunctional protein PutA1.5.5.20.441
1xddAAYIntegrin alpha-L/0.441
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.441
2xb9XNW3-dehydroquinate dehydratase4.2.1.100.441
3iobA4DPantothenate synthetase6.3.2.10.441
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.441
3tdj3TJGlutamate receptor 2/0.441
4ft5H2KSerine/threonine-protein kinase Chk12.7.11.10.441
4hdhATPGenome polyprotein2.7.7.480.441
4y3qF02Endothiapepsin3.4.23.220.441
3vw7VPXProteinase-activated receptor 1/0.441
1dq9HMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.440
1n7hNDPGDP-mannose 4,6 dehydratase 24.2.1.470.440
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.440
2e94364Geranylgeranyl pyrophosphate synthase/0.440
2opnSUFFarnesyl pyrophosphate synthase2.5.1.100.440
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.440
2vceU2FUDP-glycosyltransferase 72B1/0.440
2zi53L1Deoxycytidine kinase2.7.1.740.440
3axbFADPutative oxidoreductase/0.440
3ekuCY9Actin-5C/0.440
3fnlSHALactoperoxidase/0.440
3h3sH15Collagen type IV alpha-3-binding protein/0.440
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.440
3zm5IGMUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.440
4e03ADPPlasmid partitioning protein ParF/0.440
4g9lNGHStromelysin-13.4.24.170.440
4ikzAFSDi-tripeptide ABC transporter (Permease)/0.440
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.440
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4xg1LLPDiaminopimelate decarboxylase/0.440