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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
2q3fGNPRas-related GTP-binding protein D

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2q3fGNPRas-related GTP-binding protein D/1.000
3vhxGTPADP-ribosylation factor 6/0.528
1ky2GNPGTP-binding protein YPT7/0.526
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.520
4dzzADPPlasmid partitioning protein ParF/0.519
3mjhGTPRas-related protein Rab-5A/0.515
4y0vGDPADP-ribosylation factor 1, putative/0.515
2fg5GNPRas-related protein Rab-31/0.514
4gojGNPADP-ribosylation factor-like protein 3/0.513
3r7wGNPGTP-binding protein GTR2/0.512
3qbtGNPRas-related protein Rab-8A/0.510
4o2rGDPGTP-binding protein Rheb/0.510
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.508
4qxaGTPRas-related protein Rab-9A/0.506
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.504
4uj5GNPRas-related protein Rab-11A/0.502
1xtrGNPGTP-binding protein Rheb/0.500
5di3GNPADP-ribosylation factor-like protein 3/0.497
4fidGDPG protein alpha subunit, putative/0.496
4g01GDPRas-related protein RABF2b/0.496
1zd9GDPADP-ribosylation factor-like protein 8A/0.495
2gvdGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.495
3pcrGTPADP-ribosylation factor 6/0.495
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.494
1tu3GNPRas-related protein Rab-5A/0.494
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.494
4ylgGDPADP-ribosylation factor 1, putative/0.493
1n6lGTPRas-related protein Rab-5A/0.491
2fe4GDPRas-related protein Rab-6B/0.491
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.488
4ol0GTPGTP-binding nuclear protein Ran/0.488
5jlaNADPutative short-chain dehydrogenase/reductase/0.484
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.483
3tgpGNPGTPase HRas/0.483
1m2oGNPSmall COPII coat GTPase SAR13.6.50.482
1wdtGTPElongation factor G (EF-G-2)/0.481
1xtsGTPGTP-binding protein Rheb/0.481
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.478
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.477
5c46GSPRas-related protein Rab-11A/0.477
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.476
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.476
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.476
4fvqATPTyrosine-protein kinase JAK2/0.475
2w3bNDPDihydrofolate reductase1.5.1.30.474
3r9xGNPGTPase Era/0.474
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.474
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.474
2xtnGTPGTPase IMAP family member 2/0.473
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.471
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.471
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.471
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.471
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.471
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.471
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.469
2gilGTPRas-related protein Rab-6A/0.469
3k5dXLIBeta-secretase 13.4.23.460.469
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.468
3phiNDPShikimate dehydrogenase (NADP(+))/0.468
4h1vGNPDynamin-1-like protein3.6.5.50.468
3nbzGTPGTP-binding nuclear protein Ran/0.467
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.467
5dhaGNPGTP-binding nuclear protein Ran/0.467
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.466
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.466
2il2LIXRenin3.4.23.150.466
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.466
3uylTYDProbable NDP-rhamnosyltransferase/0.466
3qlsNDPDihydrofolate reductase1.5.1.30.465
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.464
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.464
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.463
3lpjZ75Beta-secretase 13.4.23.460.463
3oesGNPGTPase RhebL1/0.463
4lcjNADC-terminal-binding protein 2/0.463
4opgFDAConserved Archaeal protein/0.463
1eioGCHGastrotropin/0.462
3jvvACPTwitching mobility protein/0.462
3lqfNADGalactitol dehydrogenase/0.462
3tneRITCandidapepsin-13.4.23.240.462
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.461
2g247IGRenin3.4.23.150.461
2hm1LIQBeta-secretase 13.4.23.460.461
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.461
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.461
1ai9NDPDihydrofolate reductase1.5.1.30.460
1ma0NADAlcohol dehydrogenase class-31.1.1.10.460
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.460
2r9eSDXCitrate synthase2.3.3.160.460
3kb1ADPIron-sulfur cluster carrier protein/0.460
1z0aGDPRas-related protein Rab-2A/0.459
2wsbNADGalactitol dehydrogenase/0.459
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.459
1oixGDPRas-related protein Rab-11A/0.458
1v8kANPKinesin-like protein KIF2C/0.458
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.458
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.458
3tjzGNPADP-ribosylation factor 1/0.458
4dfg0JVGag-Pol polyprotein3.4.23.160.458
1dg8NDPDihydrofolate reductase1.5.1.30.457
1me6IVSPlasmepsin-23.4.23.390.457
3cphGDPRas-related protein SEC4/0.457
3r9iADPSeptum site-determining protein MinD/0.457
4e03ADPPlasmid partitioning protein ParF/0.457
4kcfAKMFAD-dependent oxidoreductase/0.457
1fm4DXCMajor pollen allergen Bet v 1-L/0.456
1ipeNDPTropinone reductase 21.1.1.2360.456
2dftADPShikimate kinase2.7.1.710.456
2ffqGSPRas-related protein Rab-6B/0.456
2rggGNPGTPase HRas/0.456
2zvcSAHPrecorrin-3 C17-methyltransferase/0.456
3kjgADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.456
1d5cGDPGTPase (Rab6)/0.455
1ia1NDPDihydrofolate reductase1.5.1.30.455
1n1eNDEGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal1.1.1.80.455
3sglFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.455
4djaFAD(6-4) photolyase/0.455
4lucGDPGTPase KRas/0.455
4uj3GNPRas-related protein Rab-11A/0.455
1szgFNSCytochrome b2, mitochondrial1.1.2.30.454
1xe55FEPlasmepsin-23.4.23.390.454
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.454
1z7yAA5Cysteine synthase 12.5.1.470.453
3ge1ADPGlycerol kinase/0.453
3kkoGNPRas-related protein M-Ras/0.453
3widNAPGlucose 1-dehydrogenase/0.453
3wqmB29Diterpene synthase3.1.7.80.453
4blrUTPNTPase P4/0.453
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.452
3b1dPLSBetaC-S lyase/0.452
3clsFADElectron transfer flavoprotein subunit alpha/0.452
3enkUPGUDP-glucose 4-epimerase/0.452
1tj2FADBifunctional protein PutA1.5.5.20.451
1vbiNADMalate/L-lactate dehydrogenase family protein/0.451
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.451
2tctCTCTetracycline repressor protein class D/0.451
3k5gBJCBeta-secretase 13.4.23.460.451
4d5gFADCyclohexane-1,2-dione hydrolase3.7.1.110.451
4v02ATPSite-determining protein/0.451
1ibrGNPGTP-binding nuclear protein Ran/0.450
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.450
2a92NAIL-lactate dehydrogenase/0.450
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
2ikuLIYRenin3.4.23.150.450
3f3sNADLambda-crystallin homolog/0.450
3mgdACOPredicted acetyltransferase/0.450
4m6jNDPDihydrofolate reductase1.5.1.30.450
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.450
1a72PADAlcohol dehydrogenase E chain1.1.1.10.449
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.449
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1u0hGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.449
2oapANPType II secretion system protein (GspE-2)/0.449
3dm5GDPSignal recognition particle 54 kDa protein/0.449
3nxxNDPDihydrofolate reductase1.5.1.30.449
3rabGNPRas-related protein Rab-3A/0.449
3toxNAPPutative oxidoreductase/0.449
4cidANPEH domain-containing protein 2/0.449
5ftcADPTPR domain protein/0.449
8dfrNDPDihydrofolate reductase1.5.1.30.449
1ef92CPMethylmalonyl-CoA decarboxylase4.1.1.410.448
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.448
1mp0NADAlcohol dehydrogenase class-31.1.1.10.448
1qorNDPQuinone oxidoreductase 1/0.448
1x7hNDPPutative ketoacyl reductase1.3.10.448
2g8yNADHydroxycarboxylate dehydrogenase B/0.448
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3keuATPPyridoxal kinase2.7.1.350.448
3refGDPRho family GTPase/0.448
4ambDUDPutative glycosyl transferase/0.448
4lpkGDPGTPase KRas/0.448
1drhNAPDihydrofolate reductase1.5.1.30.447
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.447
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.447
1x1rGDPRas-related protein M-Ras/0.447
1zbdGTPRas-related protein Rab-3A/0.447
2cig1DGDihydrofolate reductase1.5.1.30.447
2omeNADC-terminal-binding protein 2/0.447
3clrFADElectron transfer flavoprotein subunit alpha/0.447
3cosNADAlcohol dehydrogenase 41.1.1.10.447
3ijrNADOxidoreductase, short chain dehydrogenase/reductase family/0.447
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.447
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.447
4xvqGNPGTPase HRas/0.447
1hkuNADC-terminal-binding protein 11.1.10.446
1zemNADXylitol dehydrogenase/0.446
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.446
2g226IGRenin3.4.23.150.446
3cwqADPParA family chromosome partitioning protein/0.446
3k8yGNPGTPase HRas/0.446
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.446
4q73FADBifunctional protein PutA/0.446
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.446
1dr2TAPDihydrofolate reductase1.5.1.30.445
1dr3TAPDihydrofolate reductase1.5.1.30.445
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.445
3a37ADPATPase GET3/0.445
3d3wNAPL-xylulose reductase1.1.1.100.445
3gqvNAPEnoyl reductase LovC10.445
3t1tGDPProbable gliding protein mglA/0.445
3w8eNAD3-hydroxybutyrate dehydrogenase/0.445
4hdqGNPRas-related protein Rap-1b/0.445
1lbcCYZGlutamate receptor 2/0.444
1tehNADAlcohol dehydrogenase class-31.1.1.10.444
2zb3NDPProstaglandin reductase 21.3.1.480.444
3a20FMNFMN-binding protein/0.444
3dv5BAVBeta-secretase 13.4.23.460.444
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.444
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.444
4d7mTDCTetracycline repressor protein class D/0.444
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.444
4m4922YL-lactate dehydrogenase A chain1.1.1.270.444
4xd2NAIAlcohol dehydrogenase E chain1.1.1.10.444
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
5irnADPNucleotide binding oligomerization domain containing 2/0.444
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.443
1kevNDPNADP-dependent isopropanol dehydrogenase1.1.1.800.443
1uadGNPRas-related protein Ral-A/0.443
1z2aGDPRas-related protein Rab-23/0.443
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.443
2y05NAPProstaglandin reductase 1/0.443
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.443
3lpkZ76Beta-secretase 13.4.23.460.443
3qlrNDPDihydrofolate reductase1.5.1.30.443
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.443
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.443
5c3jFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.443
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.442
2g1r3IGRenin3.4.23.150.442
2hu2NADC-terminal binding protein 1/0.442
2xw7NDPDihydrofolate reductase/0.442
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
4mkgAP5Adenylate kinase/0.442
5af7FADAcyl-CoA dehydrogenase/0.442
5cypGSPSeptin-9/0.442
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.441
1gp2GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.441
1juvNDPDihydrofolate reductase1.5.1.30.441
2bpoNAPNADPH--cytochrome P450 reductase/0.441
2hfuMEVMevalonate kinase/0.441
2iko7IGRenin3.4.23.150.441
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.441
3fhyATPPyridoxal kinase2.7.1.350.441
3h2sNDPPutative NADH-flavin reductase/0.441
3h3jNADL-lactate dehydrogenase 11.1.1.270.441
3r83Z14Cyclin-dependent kinase 22.7.11.220.441
4dieC5PCytidylate kinase/0.441
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.441
4f9fGDPPutative glycosyltransferase/0.441
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.441
4qi5FADCellobiose dehydrogenase/0.441
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.440
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.440
1xs7MMIBeta-secretase 13.4.23.460.440
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.440
2qajAP5Adenylate kinase/0.440
2qbuSAHPrecorrin-2 methyltransferase/0.440
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
3pitGNPRas-related protein M-Ras/0.440
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
4e5mNAPPhosphonate dehydrogenase1.20.1.10.440
4f6w0SSCyclin-dependent kinase 82.7.11.220.440
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.440
4fm80UQBeta-secretase 13.4.23.460.440
4gl4NAIAlcohol dehydrogenase class-3/0.440
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.440
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440