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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
4dxj0M9Farnesyl pyrophosphate synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4dxj0M9Farnesyl pyrophosphate synthase/1.000
4dwb0M7Farnesyl pyrophosphate synthase/0.595
3egt722Farnesyl pyrophosphate synthase/0.575
1rqjRISFarnesyl diphosphate synthase2.5.1.100.570
3rbmB73Farnesyl pyrophosphate synthase, putative/0.560
4q23RISFarnesyl pyrophosphate synthase2.5.1.100.560
4lfvYS4Farnesyl pyrophosphate synthase2.5.1.100.559
1rqjIPEFarnesyl diphosphate synthase2.5.1.100.553
3dyh721Farnesyl pyrophosphate synthase/0.549
2f94BFQFarnesyl pyrophosphate synthase2.5.1.100.539
1zw5ZOLFarnesyl pyrophosphate synthase2.5.1.100.534
4h5dYS4Farnesyl pyrophosphate synthase2.5.1.100.527
1yq7RISFarnesyl pyrophosphate synthase2.5.1.100.526
4nkeRISFarnesyl pyrophosphate synthase2.5.1.100.524
5ero210Fusicoccadiene synthase2.5.1.290.524
1yv5RISFarnesyl pyrophosphate synthase2.5.1.100.521
3ryeUNRFarnesyl pyrophosphate synthase2.5.1.100.521
3rywK9HFarnesyl pyrophosphate synthase, putative/0.520
2opmNI9Farnesyl pyrophosphate synthase2.5.1.100.516
3krfIPEGeranyl diphosphate synthase large subunit/0.512
4kqsRISFarnesyl pyrophosphate synthase2.5.1.100.512
4h5eYS4Farnesyl pyrophosphate synthase2.5.1.100.510
2i191BYFarnesyl pyrophosphate synthase/0.504
3ez3ZOLFarnesyl pyrophosphate synthase, putative/0.503
3ldwIPEFarnesyl pyrophosphate synthase, putative/0.503
4ddhMS0Pantothenate synthetase6.3.2.10.502
2zs8ADPPantothenate kinase2.7.1.330.500
3krfDSTGeranyl diphosphate synthase large subunit/0.499
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.499
3oabDSTGeranyl diphosphate synthase large subunit/0.496
4kqsIPEFarnesyl pyrophosphate synthase2.5.1.100.496
4s26SAHPhosphomethylpyrimidine synthase, chloroplastic4.1.99.170.496
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.493
2oegUPGUDP-glucose pyrophosphorylase/0.492
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.488
2zsbADPPantothenate kinase2.7.1.330.488
4nauAGSPhosphopantetheine adenylyltransferase/0.487
1joaFADNADH peroxidase1.11.1.10.485
4qnyANPMitogen activated protein kinase, putative/0.484
3ldwZOLFarnesyl pyrophosphate synthase, putative/0.482
4lfgIPEPutative geranyltranstransferase/0.482
4jvj1MVFarnesyl pyrophosphate synthase2.5.1.100.481
1wkgPOI[LysW]-aminoadipate semialdehyde transaminase/0.480
4hmvWUBPhenazine biosynthesis protein PhzG1.40.479
5f54TMPSingle-stranded-DNA-specific exonuclease/0.478
3ea0ATPATPase, ParA family/0.477
1szfFMNCytochrome b2, mitochondrial1.1.2.30.476
1szgFNSCytochrome b2, mitochondrial1.1.2.30.476
4k10NI9Farnesyl pyrophosphate synthase/0.474
1rdwLARActin, alpha skeletal muscle/0.472
2hs0ATPPhosphoribosylformylglycinamidine synthase subunit PurL/0.472
2o12FMNChorismate synthase/0.472
3e8xNAPBH1520 protein/0.472
2trtTACTetracycline repressor protein class D/0.471
3iczPB6Farnesyl pyrophosphate synthase/0.470
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.470
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.470
1n0sFLUBilin-binding protein/0.469
1vzbUMPThymidylate synthase/0.469
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.468
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.467
3hyoADPPyridoxal kinase/0.467
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.467
1gotGDPGuanine nucleotide-binding protein G(t) subunit alpha-1/0.466
1njeDCMThymidylate synthase/0.466
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.466
3vhxGTPADP-ribosylation factor 6/0.466
1w34FADFerredoxin--NADP reductase1.18.1.20.465
2gesCOKPantothenate kinase2.7.1.330.465
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.465
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.465
5cwa0GAAnthranilate synthase component 14.1.3.270.465
1nhqFADNADH peroxidase1.11.1.10.464
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.464
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.464
4m2bUPGUDP-glucose pyrophosphorylase/0.464
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.464
5aqzSGVHeat shock 70 kDa protein 1A/0.464
1jedADPSulfate adenylyltransferase/0.463
1vgrCOAFormyl-CoA:oxalate CoA-transferase/0.463
3hf3FMNChromate reductase/0.463
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.462
1njdUMPThymidylate synthase/0.462
2e93B29Geranylgeranyl pyrophosphate synthase/0.462
2qo9ANPEphrin type-A receptor 32.7.10.10.462
2xf3J01Uncharacterized protein/0.462
1n2gAPCPantothenate synthetase6.3.2.10.461
1nhpFADNADH peroxidase1.11.1.10.461
2oatPFMOrnithine aminotransferase, mitochondrial2.6.1.130.461
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.461
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.461
3ta1ADPNitrogen regulatory protein P-II (GlnB-3)/0.461
4e2xTYDMethyltransferase/0.461
1bcpATPPertussis toxin subunit 4/0.460
1bcpATPPertussis toxin subunit 5/0.460
3enkUPGUDP-glucose 4-epimerase/0.460
3g0gRUMDipeptidyl peptidase 4/0.460
3rv9RVDSalicylate synthase/0.460
1f8wFADNADH peroxidase1.11.1.10.459
1kh2ATPArgininosuccinate synthase/0.459
1w5sADPORC1-type DNA replication protein 2/0.459
2bx8AZQSerum albumin/0.459
3ivgFG5Pantothenate synthetase6.3.2.10.459
2tctCTCTetracycline repressor protein class D/0.458
3af1GDPPantothenate kinase2.7.1.330.458
3cisATPUniversal stress protein Rv2623/0.458
3clrFADElectron transfer flavoprotein subunit alpha/0.458
3ez3IPEFarnesyl pyrophosphate synthase, putative/0.458
3lqsPSZD-alanine aminotransferase2.6.1.210.458
1j21ATPArgininosuccinate synthase/0.457
1z48FMNNADPH dehydrogenase/0.457
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.457
2e8tIPEGeranylgeranyl pyrophosphate synthase/0.457
2opnSUFFarnesyl pyrophosphate synthase2.5.1.100.457
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.457
3tr05GPGuanylate kinase/0.457
4loh1SYStimulator of interferon genes protein/0.457
1g9dBABBotulinum neurotoxin type B3.4.24.690.456
1icsFMN12-oxophytodienoate reductase 11.3.1.420.456
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.456
2qtrNXXProbable nicotinate-nucleotide adenylyltransferase/0.456
3r7wGNPGTP-binding protein GTR2/0.456
3sixGDPNodulation protein Z/0.456
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.456
4m2aUPGUDP-glucose pyrophosphorylase/0.456
1ef92CPMethylmalonyl-CoA decarboxylase4.1.1.410.455
1j7uANPAminoglycoside 3'-phosphotransferase2.7.1.950.455
1ky2GNPGTP-binding protein YPT7/0.455
1n2eAPCPantothenate synthetase6.3.2.10.455
2uz3TTPThymidine kinase/0.455
2xvu9DNSerum albumin/0.455
3qi2GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.455
3tjzGNPADP-ribosylation factor 1/0.455
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.455
4f5dC2EStimulator of interferon genes protein/0.455
4loi1YCStimulator of interferon genes protein/0.455
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.454
1kbiFMNCytochrome b2, mitochondrial1.1.2.30.454
3dj4UD1Bifunctional protein GlmU/0.454
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.454
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.454
3q9lATPSeptum site-determining protein MinD/0.454
4i9aNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]/0.454
4j7uNAPSepiapterin reductase1.1.1.1530.454
4k28NADShikimate dehydrogenase family protein/0.454
5choFADFlavin reductase/0.454
1xjwPALAspartate carbamoyltransferase catalytic subunit2.1.3.20.453
2nnqT4BFatty acid-binding protein, adipocyte/0.453
3ivxFG6Pantothenate synthetase6.3.2.10.453
3w8rACPUridine kinase/0.453
4mb2ATPUncharacterized protein/0.453
4psbGA3Cytokinin-specific binding protein/0.453
4xguADPPutative pachytene checkpoint protein 2/0.453
5kwvANPPantothenate synthetase/0.453
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.452
2lbaCHOFatty acid binding protein 6/0.452
3a37ADPATPase GET3/0.452
3intGDUUDP-galactopyranose mutase5.4.99.90.452
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.452
4hdhATPGenome polyprotein2.7.7.480.452
1qrsATPGlutamine--tRNA ligase6.1.1.180.451
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.451
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.451
1wkhPPE[LysW]-aminoadipate semialdehyde transaminase/0.451
2tdmUMPThymidylate synthase/0.451
2x3jATPAcsD/0.451
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.451
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.451
4df2FMNNADPH dehydrogenase/0.451
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.451
4oagADPMitochondrial dynamics protein MID51/0.451
4ohwATPProtein clpf-1/0.451
5agaANPDNA polymerase theta/0.451
1u3dFADCryptochrome-1/0.450
2ej2PPEBranched-chain amino acid aminotransferase (IlvE)/0.450
3c212BADNA integrity scanning protein DisA/0.450
3fvlBHKCarboxypeptidase A13.4.17.10.450
3ldp3P178 kDa glucose-regulated protein/0.450
3muoZPRProlyl endopeptidase/0.450
3zgfIUGHisto-blood group ABO system transferase/0.450
4a6aTTPdCTP deaminase3.5.4.130.450
4e03ADPPlasmid partitioning protein ParF/0.450
5iqiGNPBifunctional AAC/APH2.3.10.450
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.449
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.449
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.449
1i5aACPChemotaxis protein CheA2.7.13.30.449
1nzq162Prothrombin3.4.21.50.449
1p0hACOMycothiol acetyltransferase2.3.1.1890.449
1p52ADPArginine kinase2.7.3.30.449
1rq1FADEndoplasmic oxidoreductin-11.8.40.449
2e94364Geranylgeranyl pyrophosphate synthase/0.449
2vkvTDCTetracycline repressor protein class D/0.449
2zseACPPantothenate kinase2.7.1.330.449
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.449
4bqwQNMEgl nine homolog 1/0.449
1f3bGBXGlutathione S-transferase A12.5.1.180.448
1g0rTHMGlucose-1-phosphate thymidylyltransferase/0.448
1gvrTNLPentaerythritol tetranitrate reductase/0.448
1p3dUMAUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.448
2pbzATPUncharacterized protein/0.448
2wezZYEBeta-secretase 13.4.23.460.448
3cl2G39Neuraminidase/0.448
3g0bT22Dipeptidyl peptidase 4/0.448
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.448
3q7fED2Uncharacterized protein/0.448
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.448
1icpFMN12-oxophytodienoate reductase 11.3.1.420.447
1uopGLY_PHE_GLU_PROProlyl endopeptidase3.4.21.260.447
1z0dGDPRas-related protein Rab-5C/0.447
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.447
2q4bNAPUncharacterized protein At5g02240/0.447
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.447
3efwAK8Aurora kinase A2.7.11.10.447
3pjuC2EDiguanylate cyclase/phosphodiesterase/0.447
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.447
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.446
1esmCOAPantothenate kinase2.7.1.330.446
1jwtBLIProthrombin3.4.21.50.446
1qiqACCIsopenicillin N synthase1.21.3.10.446
1rpnNDPGDP-mannose 4,6-dehydratase/0.446
2gr1FADFerredoxin reductase/0.446
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.446
2xb5I7TTetracycline repressor protein class D/0.446
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.446
3gwdNAPCyclohexanone monooxygenase/0.446
3l67FMNXenobiotic reductase/0.446
3pi0F91Endothiapepsin3.4.23.220.446
4h4wFADBiphenyl dioxygenase ferredoxin reductase subunit/0.446
4lb9EVPSerum albumin/0.446
4o2rGDPGTP-binding protein Rheb/0.446
1evjNADGlucose--fructose oxidoreductase1.1.99.280.445
1i6kTYMTryptophan--tRNA ligase6.1.1.20.445
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2oz57XYUncharacterized protein/0.445
2wtkANPSTE20-related kinase adapter protein alpha/0.445
2wvjTTPThymidine kinase, cytosolic2.7.1.210.445
2wzvFMNNitroreductase NfnB/0.445
2z95NDPGDP-mannose 4,6-dehydratase/0.445
3pfiADPHolliday junction ATP-dependent DNA helicase RuvB/0.445
3sdkP3NProteasome subunit beta type-53.4.25.10.445
3sdkP3NProteasome subunit beta type-63.4.25.10.445
3vtkADPThymidine kinase/0.445
3wb2YGPUncharacterized protein MJ0488/0.445
4dzzADPPlasmid partitioning protein ParF/0.445
4j57FADThioredoxin reductase 21.8.1.90.445
4nxuADPMitochondrial dynamics protein MID51/0.445
4qaiFMNNADPH dehydrogenase/0.445
1dgfNDPCatalase1.11.1.60.444
1r5hAO2Methionine aminopeptidase 2/0.444
1xtsGTPGTP-binding protein Rheb/0.444
2an9GDPGuanylate kinase2.7.4.80.444
4c4oNADSADH/0.444
4fx9COACoenzyme A disulfide reductase1.8.1.140.444
4fxfATPPyruvate kinase PKM2.7.1.400.444
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.444
4uz6SCRPalmitoleoyl-protein carboxylesterase NOTUM/0.444
5d3qGDPDynamin-13.6.5.50.444
1e8hADPVanillyl-alcohol oxidase1.1.3.380.443
1ek5NADUDP-glucose 4-epimerase/0.443
1eq2NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.443
1i59ANPChemotaxis protein CheA2.7.13.30.443
1i7lATPSynapsin-2/0.443
1pmn984Mitogen-activated protein kinase 102.7.11.240.443
1uooGLY_PHE_ARG_PROProlyl endopeptidase3.4.21.260.443
1xdpATPPolyphosphate kinase/0.443
2ffqGSPRas-related protein Rab-6B/0.443
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.443
3dl0AP5Adenylate kinase/0.443
3ndjJHZMethyltransferase/0.443
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.443
3wbzATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980}/0.443
4ikzAFSDi-tripeptide ABC transporter (Permease)/0.443
4j7xNAPSepiapterin reductase1.1.1.1530.443
4jyzATPGlutamine--tRNA ligase6.1.1.180.443
4rpjFADUDP-galactopyranose mutase5.4.99.90.443
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.443
1n0hCIEAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.442
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
1oixGDPRas-related protein Rab-11A/0.442
1s4oGDPGlycolipid 2-alpha-mannosyltransferase/0.442
1sb8UD2WbpP/0.442
2clsGTPRho-related GTP-binding protein Rho6/0.442
2cv1ATPGlutamate--tRNA ligase6.1.1.170.442
2e77FMNLactate oxidase/0.442
2e8wIPEGeranylgeranyl pyrophosphate synthase/0.442
2fe4GDPRas-related protein Rab-6B/0.442
2oahQINBeta-secretase 13.4.23.460.442
2q46NAPUncharacterized protein At5g02240/0.442
2r7pANPNon-structural protein 23.6.40.442
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.442
2zt5B4PGlycine--tRNA ligase/0.442
3aezGDPPantothenate kinase2.7.1.330.442
3b6pTMPThree-prime repair exonuclease 13.1.11.20.442
3eq02TSProthrombin3.4.21.50.442
3hgrFMN12-oxophytodienoate reductase 11.3.1.420.442
3ivmZPRProlyl endopeptidase/0.442
3p62FMNPentaerythritol tetranitrate reductase/0.442
3p84FMNPentaerythritol tetranitrate reductase/0.442
3qttANPPantothenate synthetase/0.442
3r9iADPSeptum site-determining protein MinD/0.442
3tzaTZGGlutamate receptor 2/0.442
4cqnILALeucine--tRNA ligase/0.442
4iijGTPTubulin alpha-1B chain/0.442
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.442
4oztP1AEcdysone receptor, putative/0.442
1bxqPP8Penicillopepsin-13.4.23.200.441
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.441
1hb1OCVIsopenicillin N synthase1.21.3.10.441
1npxFADNADH peroxidase1.11.1.10.441
1u28NAPNAD(P) transhydrogenase subunit beta1.6.1.20.441
2e91ZOLGeranylgeranyl pyrophosphate synthase/0.441
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.441
2wb2FADRE11660p/0.441
2zrjAGSProtein RecA/0.441
2zs9ADPPantothenate kinase2.7.1.330.441
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.441
4avlTMPPolymerase acidic protein/0.441
4baoMVFProthrombin3.4.21.50.441
4fidGDPG protein alpha subunit, putative/0.441
4fzvSAM5-methylcytosine rRNA methyltransferase NSUN42.1.10.441
4nxwADPMitochondrial dynamics protein MID51/0.441
4rx6ATPNitrogen regulatory PII-like protein/0.441
5a02NAPGlucose-fructose oxidoreductase/0.441
1c7oPPGHemolysin/0.440
1fyfSSAThreonine--tRNA ligase6.1.1.30.440
1jdbADPCarbamoyl-phosphate synthase large chain/0.440
1jstATPCyclin-dependent kinase 22.7.11.220.440
1orrCDPCDP-paratose 2-epimerase/0.440
1xjqADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.440
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.440
1yzqGNPRas-related protein Rab-6A/0.440
2e2qADPATP-dependent hexokinase/0.440
2hfuMEVMevalonate kinase/0.440
2nyaMGDPeriplasmic nitrate reductase1.7.99.40.440
2v5aLZLBiotin carboxylase6.3.4.140.440
2wf1ZY1Beta-secretase 13.4.23.460.440
2zc922UProthrombin3.4.21.50.440
3af0GDPPantothenate kinase2.7.1.330.440
3bgxTMPThymidylate synthase/0.440
3cluFADElectron transfer flavoprotein subunit alpha/0.440
3dm5GDPSignal recognition particle 54 kDa protein/0.440
3f3sNADLambda-crystallin homolog/0.440
3tdj3TJGlutamate receptor 2/0.440
3w233RODihydroorotate dehydrogenase (fumarate)1.3.98.10.440
4kqqVPPPeptidoglycan D,D-transpeptidase FtsI/0.440
4uyf73BBromodomain-containing protein 2/0.440
5dozNDPJamJ/0.440
6tmn0PIThermolysin3.4.24.270.440