Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3bbfGDPNucleoside diphosphate kinase B2.7.4.6

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3bbfGDPNucleoside diphosphate kinase B2.7.4.61.000
1nueGDPNucleoside diphosphate kinase B2.7.4.60.610
2hveADPNucleoside diphosphate kinase A2.7.4.60.602
2hvdADPNucleoside diphosphate kinase A2.7.4.60.597
4uofDATNucleoside diphosphate kinase/0.565
4uohADPNucleoside diphosphate kinase/0.558
4uogYYYNucleoside diphosphate kinase/0.545
4fkxCDPNucleoside diphosphate kinase/0.542
1be4PCGNucleoside diphosphate kinase A 22.7.4.60.512
3q8uADPNucleoside diphosphate kinase/0.509
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.502
4twnB96Ephrin type-A receptor 32.7.10.10.501
2ydvNECAdenosine receptor A2a/0.499
4uhrNGIAdenosine receptor A2a/0.499
3nguADPNucleoside diphosphate kinase/0.496
4dvi2IWTankyrase-12.4.2.300.496
1wklATPNucleoside diphosphate kinase/0.494
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.490
5k2aZMAAdenosine receptor A2a/0.489
4iaq2GM5-hydroxytryptamine receptor 1B/0.488
5k2cZMAAdenosine receptor A2a/0.487
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.486
1oc1ASVIsopenicillin N synthase1.21.3.10.485
3vg9ZMAAdenosine receptor A2a/0.485
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.485
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.484
4jlj1NMDeoxycytidine kinase2.7.1.740.483
4tlaADPCircadian clock protein kinase KaiC2.7.11.10.482
5iu4ZMAAdenosine receptor A2a/0.482
4tleAGSCircadian clock protein kinase KaiC2.7.11.10.481
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.480
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.479
3qakUKAAdenosine receptor A2a/0.479
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.478
1dr4HBIDihydrofolate reductase1.5.1.30.477
1hb3SCVIsopenicillin N synthase1.21.3.10.476
2dxeGDPNucleoside diphosphate kinase2.7.4.60.475
1lwlDSOCamphor 5-monooxygenase1.14.15.10.474
4at5MUJBDNF/NT-3 growth factors receptor2.7.10.10.474
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.474
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.473
1obnASVIsopenicillin N synthase1.21.3.10.472
4eiyZMAAdenosine receptor A2a/0.472
2g78REACellular retinoic acid-binding protein 2/0.471
4tl9AGSCircadian clock protein kinase KaiC2.7.11.10.471
5jtbZMAAdenosine receptor A2a/0.471
1pd9CO4Dihydrofolate reductase1.5.1.30.470
3arvSAUChitinase A/0.470
1dljUGAUDP-glucose 6-dehydrogenase/0.469
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.469
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.469
5k2bZMAAdenosine receptor A2a/0.469
1dliUDXUDP-glucose 6-dehydrogenase/0.468
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.468
5dp2NAPCurF/0.468
4ug2NGIAdenosine receptor A2a/0.468
2be2R22Gag-Pol polyprotein2.7.7.490.467
4bfuZVUPantothenate kinase2.7.1.330.467
2az3CDPNucleoside diphosphate kinase/0.466
2vcmM11Isopenicillin N synthase1.21.3.10.466
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
1qiqACCIsopenicillin N synthase1.21.3.10.465
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.465
3jzmATPCircadian clock protein kinase KaiC2.7.11.10.465
2wo7ASVIsopenicillin N synthase1.21.3.10.464
3vo30KFVascular endothelial growth factor receptor 22.7.10.10.464
5iubCLRAdenosine receptor A2a/0.464
5iu86DZAdenosine receptor A2a/0.464
2ydoADNAdenosine receptor A2a/0.463
3g0eB49Mast/stem cell growth factor receptor Kit2.7.10.10.463
3wv9FEGHmd co-occurring protein HcgE/0.463
5k2dZMAAdenosine receptor A2a/0.463
1efaNPFLactose operon repressor/0.462
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.462
2vbdV10Isopenicillin N synthase1.21.3.10.462
1hb1OCVIsopenicillin N synthase1.21.3.10.461
1qjfACSIsopenicillin N synthase1.21.3.10.461
1x8b824Wee1-like protein kinase2.7.10.20.461
3tfn2CJDehydrosqualene synthase/0.461
2in6839Wee1-like protein kinase2.7.10.20.460
2vbpVB1Isopenicillin N synthase1.21.3.10.460
3zoiM2WIsopenicillin N synthase1.21.3.10.460
5uviZMAAdenosine receptor A2a/0.460
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.459
2z2w770Wee1-like protein kinase2.7.10.20.459
3zkyWT4Isopenicillin N synthase1.21.3.10.459
1pqc444Oxysterols receptor LXR-beta/0.458
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.458
2dxfGNPNucleoside diphosphate kinase2.7.4.60.458
2uxpCLMHTH-type transcriptional regulator TtgR/0.458
3k9vCPS1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial/0.458
3p0fBAUUridine phosphorylase 22.4.2.30.458
3reyXACAdenosine receptor A2a/0.458
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.457
1ygjRMCPyridoxal kinase2.7.1.350.457
2jb4A14Isopenicillin N synthase1.21.3.10.457
3dvlATPCircadian clock protein kinase KaiC2.7.11.10.457
3k0fATPCircadian clock protein kinase KaiC2.7.11.10.457
3s1aATPCircadian clock protein kinase KaiC2.7.11.10.457
4qi9MTXDihydrofolate reductase/0.457
5iqbGNPBifunctional AAC/APH2.3.10.457
5iua6DXAdenosine receptor A2a/0.457
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.456
1z6tADPApoptotic protease-activating factor 1/0.456
3junAKDPhenazine biosynthesis protein A/B/0.456
3q43D66M1 family aminopeptidase3.4.110.456
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
3thrC2FGlycine N-methyltransferase2.1.1.200.456
5iqaGNPBifunctional AAC/APH2.3.10.456
5g53NECAdenosine receptor A2a/0.456
1d2sDHTSex hormone-binding globulin/0.455
2e94364Geranylgeranyl pyrophosphate synthase/0.455
2ejzSAHDiphthine synthase/0.455
2g2hP16Tyrosine-protein kinase ABL12.7.10.20.455
2pmnK51Protein kinase 7/0.455
3cqeP91Wee1-like protein kinase2.7.10.20.455
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.455
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
4rh10TTSpore photoproduct lyase/0.455
1qpePP2Tyrosine-protein kinase Lck2.7.10.20.454
2rabNADGlutathione amide reductase/0.454
3gi2GHWDihydrofolate reductase1.5.1.30.454
3p9tTCLRepressor/0.454
3up3XCAaceDAF-12/0.454
5d0rB1TAdenylate cyclase type 10/0.454
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1xzqFONtRNA modification GTPase MnmE3.6.50.453
2iviACWIsopenicillin N synthase1.21.3.10.453
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.453
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.453
3havATPAminoglycoside phosphotransferase/0.453
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
4a8v2ANMajor pollen allergen Bet v 1-J/0.453
4l17DNQGlutamate receptor 2/0.453
4tl8AGSCircadian clock protein kinase KaiC2.7.11.10.453
1tslA15Thymidylate synthase/0.452
2bf7HBIPteridine reductase 11.5.1.330.452
2gfsPQBMitogen-activated protein kinase 14/0.452
3cr0809Wee1-like protein kinase2.7.10.20.452
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3up0D7SaceDAF-12/0.452
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
4a84DXCMajor pollen allergen Bet v 1-A/0.452
1bk0ACVIsopenicillin N synthase1.21.3.10.451
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.451
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.451
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.60.451
1xddAAYIntegrin alpha-L/0.451
2bu9HFVIsopenicillin N synthase1.21.3.10.451
2dy9ADPNucleoside diphosphate kinase2.7.4.60.451
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.451
2gtnLIEMitogen-activated protein kinase 14/0.451
2xuiTZ5Acetylcholinesterase3.1.1.70.451
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.451
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.451
3emlZMAAdenosine receptor A2a/0.451
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.450
1w7kADPDihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.450
2bifANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 42.7.1.1050.450
2cleF6FTryptophan synthase alpha chain/0.450
2fb35ADGTP 3',8-cyclase4.1.99.180.450
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.450
3drcMTXDihydrofolate reductase1.5.1.30.450
3lpfZ77Beta-glucuronidase3.2.1.310.450
3pyzANPDihydrofolate synthase/folylpolyglutamate synthase/0.450
4h4o506Gag-Pol polyprotein2.7.7.490.450
4idpGNPAtlastin-13.6.50.450
4knzCB3Thymidylate synthase/0.450
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
1crbRTLRetinol-binding protein 1/0.449
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.449
2y60M8FIsopenicillin N synthase1.21.3.10.449
3bx5304Mitogen-activated protein kinase 14/0.449
3uvvREARetinoic acid receptor RXR-alpha/0.449
4bb3KKAIsopenicillin N synthase1.21.3.10.449
4tlcAGSCircadian clock protein kinase KaiC2.7.11.10.449
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.449
5il2SAHN6-adenosine-methyltransferase 70 kDa subunit/0.449
1kkq471Peroxisome proliferator-activated receptor alpha/0.448
1mvtDTMDihydrofolate reductase1.5.1.30.448
1uzwCDHIsopenicillin N synthase1.21.3.10.448
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.448
2ji6ADPOxalyl-CoA decarboxylase4.1.1.80.448
2ofv242Tyrosine-protein kinase Lck2.7.10.20.448
2pckSAHDiphthine synthase/0.448
2pdtFADVivid PAS protein VVD/0.448
3csoXNIGenome polyprotein2.7.7.480.448
3ehjACPSensor histidine kinase DesK2.7.13.30.448
3lv1NAPNAD(P)-dependent benzaldehyde dehydrogenase1.2.1.280.448
3occDIHPurine nucleoside phosphorylase DeoD-type/0.448
3vt5YI2Vitamin D3 receptor/0.448
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
1nhkCMPNucleoside diphosphate kinase2.7.4.60.447
1upw444Oxysterols receptor LXR-beta/0.447
2w3aTOPDihydrofolate reductase1.5.1.30.447
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
3acy702Dehydrosqualene synthase/0.447
3lalKRVGag-Pol polyprotein2.7.7.490.447
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.447
2gpuOHTEstrogen-related receptor gamma/0.446
2gqfFADUncharacterized protein HI_0933/0.446
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
4a86H35Major pollen allergen Bet v 1-A/0.446
4kak06UDihydrofolate reductase1.5.1.30.446
1cbqRE9Cellular retinoic acid-binding protein 2/0.445
1df8BTNStreptavidin/0.445
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.445
1xuoLA1Integrin alpha-L/0.445
2dxxSAHDiphthine synthase/0.445
2g44T3OEstrogen receptor/0.445
2xvhFADPutative flavin-containing monooxygenase/0.445
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.445
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4b2gV1NUncharacterized protein/0.445
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.445
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.445
4orkGDPBifunctional AAC/APH2.3.10.445
4oztP1AEcdysone receptor, putative/0.445
8catNDPCatalase1.11.1.60.445
1dhjMTXDihydrofolate reductase1.5.1.30.444
1kruIPTGalactoside O-acetyltransferase2.3.1.180.444
1lcoPPYCytochrome b2, mitochondrial1.1.2.30.444
2a9z26AAdenosine kinase2.7.1.200.444
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.444
4a87NARMajor pollen allergen Bet v 1-A/0.444
4b8mVX6Aurora kinase B-A2.7.11.10.444
4dymIYZActivin receptor type-12.7.11.300.444
4lgh0JNProto-oncogene tyrosine-protein kinase Src2.7.10.20.444
1v9aSAHUncharacterized protein/0.443
1ygkRRCPyridoxal kinase2.7.1.350.443
2hziJINTyrosine-protein kinase ABL12.7.10.20.443
2oh4GIGVascular endothelial growth factor receptor 22.7.10.10.443
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.443
3ghwGHWDihydrofolate reductase1.5.1.30.443
3ielU5PRibonuclease TTHA02523.10.443
3oafOAGDihydrofolate reductase1.5.1.30.443
3qpvADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.443
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.443
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.443
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.443
4rbs0RVMetallo-beta-lactamase type 2/0.443
4z87GDPInosine-5'-monophosphate dehydrogenase/0.443
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.443
3pwhZMAAdenosine receptor A2a/0.443
1hfqMOTDihydrofolate reductase1.5.1.30.442
1mp0NADAlcohol dehydrogenase class-31.1.1.10.442
2iutAGSDNA translocase FtsK/0.442
2j9lATPH(+)/Cl(-) exchange transporter 5/0.442
2vroNDP3,4-dehydroadipyl-CoA semialdehyde dehydrogenase/0.442
2ykjYKJHeat shock protein HSP 90-alpha/0.442
3arpDEQChitinase A/0.442
3bgxMEFThymidylate synthase/0.442
3d4bDZDNAD-dependent protein deacetylase/0.442
3k4nFADPyranose 2-oxidase/0.442
3mtfA3FActivin receptor type-12.7.11.300.442
3nbzGTPGTP-binding nuclear protein Ran/0.442
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.442
3njoPYVAbscisic acid receptor PYR1/0.442
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.442
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.442
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.442
4l5b1UXDeoxycytidine kinase2.7.1.740.442
3uzcT4EAdenosine receptor A2a/0.442
1cbrREACellular retinoic acid-binding protein 1/0.441
1e2jTHMThymidine kinase/0.441
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1t48BB3Tyrosine-protein phosphatase non-receptor type 13.1.3.480.441
1trgCB3Thymidylate synthase/0.441
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.441
2bgjFADNADPH:ferredoxin reductase/0.441
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.441
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.441
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.441
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.441
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.441
3gkjHC3Niemann-Pick C1 protein/0.441
3nmpPYVAbscisic acid receptor PYL2/0.441
3tl1JROPutative polyketide cyclase/0.441
3vf60H6Glucokinase2.7.1.20.441
4at0FADPossible succinate dehydrogenase/0.441
4jlk1NODeoxycytidine kinase2.7.1.740.441
4r20AERCytochrome P450 family 17 polypeptide 2/0.441
5ej7TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.441
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.440
1m67BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal1.1.1.80.440
1mj3HXCEnoyl-CoA hydratase, mitochondrial4.2.1.170.440
2e07SAHDiphthine synthase/0.440
3dmjGWEPol protein/0.440
3fpjSAMUncharacterized protein/0.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3jziJZLBiotin carboxylase6.3.4.140.440
3nwlNDPCatalase1.11.1.60.440
3of3DIHPurine nucleoside phosphorylase DeoD-type 1/0.440
3vo2FADFerredoxin--NADP reductase/0.440
4b4vL34Bifunctional protein FolD/0.440
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.440
5dozNDPJamJ/0.440