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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3bbfGDPNucleoside diphosphate kinase B2.7.4.6

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3bbfGDPNucleoside diphosphate kinase B2.7.4.61.000
2hveADPNucleoside diphosphate kinase A2.7.4.60.601
1nueGDPNucleoside diphosphate kinase B2.7.4.60.589
4uohADPNucleoside diphosphate kinase/0.561
4uofDATNucleoside diphosphate kinase/0.550
4uogYYYNucleoside diphosphate kinase/0.534
4fkxCDPNucleoside diphosphate kinase/0.526
2ydvNECAdenosine receptor A2a/0.506
4uhrNGIAdenosine receptor A2a/0.503
3q8uADPNucleoside diphosphate kinase/0.499
3uzcT4EAdenosine receptor A2a/0.489
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.487
4twnB96Ephrin type-A receptor 32.7.10.10.487
3nguADPNucleoside diphosphate kinase/0.485
2ydoADNAdenosine receptor A2a/0.484
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.484
5iu4ZMAAdenosine receptor A2a/0.484
4iaq2GM5-hydroxytryptamine receptor 1B/0.483
5k2aZMAAdenosine receptor A2a/0.483
1wklATPNucleoside diphosphate kinase/0.481
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.479
5k2cZMAAdenosine receptor A2a/0.479
3vg9ZMAAdenosine receptor A2a/0.478
4eiyZMAAdenosine receptor A2a/0.476
4dvi2IWTankyrase-12.4.2.300.475
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.473
3emlZMAAdenosine receptor A2a/0.473
4ug2NGIAdenosine receptor A2a/0.471
1dr4HBIDihydrofolate reductase1.5.1.30.468
3up0D7SaceDAF-12/0.468
3uzaT4GAdenosine receptor A2a/0.467
2be2R22Gag-Pol polyprotein2.7.7.490.466
2g78REACellular retinoic acid-binding protein 2/0.466
4ffrATPUncharacterized protein/0.466
4tlaADPCircadian clock protein kinase KaiC2.7.11.10.466
3qakUKAAdenosine receptor A2a/0.466
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.465
4at5MUJBDNF/NT-3 growth factors receptor2.7.10.10.465
5jtbZMAAdenosine receptor A2a/0.465
5iu86DZAdenosine receptor A2a/0.464
1obnASVIsopenicillin N synthase1.21.3.10.463
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.463
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.463
5dp2NAPCurF/0.463
2dxeGDPNucleoside diphosphate kinase2.7.4.60.462
4qi9MTXDihydrofolate reductase/0.462
4z87GDPInosine-5'-monophosphate dehydrogenase/0.461
3wv9FEGHmd co-occurring protein HcgE/0.460
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
4ug7H4BNitric oxide synthase oxygenase1.14.13.1650.460
1gpeFADGlucose oxidase1.1.3.40.458
3tfn2CJDehydrosqualene synthase/0.458
5k2bZMAAdenosine receptor A2a/0.458
5k2dZMAAdenosine receptor A2a/0.457
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.456
1lwlDSOCamphor 5-monooxygenase1.14.15.10.456
1oc1ASVIsopenicillin N synthase1.21.3.10.456
3cqeP91Wee1-like protein kinase2.7.10.20.456
3cr0809Wee1-like protein kinase2.7.10.20.456
3s1aATPCircadian clock protein kinase KaiC2.7.11.10.456
4fx9FADCoenzyme A disulfide reductase1.8.1.140.456
3havATPAminoglycoside phosphotransferase/0.455
1dljUGAUDP-glucose 6-dehydrogenase/0.454
1ygjRMCPyridoxal kinase2.7.1.350.454
3njoPYVAbscisic acid receptor PYR1/0.454
4fflADPUncharacterized protein/0.454
5d5bCAUBeta-2 adrenergic receptor/0.454
2az3CDPNucleoside diphosphate kinase/0.453
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.453
1bk0ACVIsopenicillin N synthase1.21.3.10.452
2dxxSAHDiphthine synthase/0.452
2in6839Wee1-like protein kinase2.7.10.20.452
2z2w770Wee1-like protein kinase2.7.10.20.452
3arvSAUChitinase A/0.452
3g0eB49Mast/stem cell growth factor receptor Kit2.7.10.10.452
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.452
5iubCLRAdenosine receptor A2a/0.452
1dliUDXUDP-glucose 6-dehydrogenase/0.451
1efaNPFLactose operon repressor/0.451
1q3hANPCystic fibrosis transmembrane conductance regulator/0.451
2zi53L1Deoxycytidine kinase2.7.1.740.451
3b9lAZZSerum albumin/0.451
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.451
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.60.450
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.450
2huqSAHDiphthine synthase/0.450
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.450
3fpjSAMUncharacterized protein/0.450
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
3zkyWT4Isopenicillin N synthase1.21.3.10.450
4nbb9CATerminal oxygenase component of carbazole/0.450
4oztP1AEcdysone receptor, putative/0.450
5iua6DXAdenosine receptor A2a/0.450
1crbRTLRetinol-binding protein 1/0.449
2ejzSAHDiphthine synthase/0.449
2pckSAHDiphthine synthase/0.448
3mjrAC2Deoxycytidine kinase2.7.1.740.448
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.447
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.447
3vo30KFVascular endothelial growth factor receptor 22.7.10.10.447
1uymPU3Heat shock protein HSP 90-beta/0.446
1x8b824Wee1-like protein kinase2.7.10.20.446
2dxfGNPNucleoside diphosphate kinase2.7.4.60.446
2e07SAHDiphthine synthase/0.446
2xuiTZ5Acetylcholinesterase3.1.1.70.446
2ykjYKJHeat shock protein HSP 90-alpha/0.446
3jzmATPCircadian clock protein kinase KaiC2.7.11.10.446
4nbh9CATerminal oxygenase component of carbazole/0.446
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.445
3p0fBAUUridine phosphorylase 22.4.2.30.445
1hb1OCVIsopenicillin N synthase1.21.3.10.444
1me6IVSPlasmepsin-23.4.23.390.444
1qpePP2Tyrosine-protein kinase Lck2.7.10.20.444
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.444
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.444
2pmnK51Protein kinase 7/0.444
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.444
2xvhFADPutative flavin-containing monooxygenase/0.444
3up3XCAaceDAF-12/0.444
4h380YXDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
4kwi1TJReductase homolog/0.444
5iqaGNPBifunctional AAC/APH2.3.10.444
5iqbGNPBifunctional AAC/APH2.3.10.444
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.443
1z6tADPApoptotic protease-activating factor 1/0.443
4tlbAGSCircadian clock protein kinase KaiC2.7.11.10.443
1nbiSAMGlycine N-methyltransferase2.1.1.200.442
2iviACWIsopenicillin N synthase1.21.3.10.442
2uxpCLMHTH-type transcriptional regulator TtgR/0.442
2vbpVB1Isopenicillin N synthase1.21.3.10.442
3gi2GHWDihydrofolate reductase1.5.1.30.442
3reoEUG(Iso)eugenol O-methyltransferase2.1.1.1460.442
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.442
4bfuZVUPantothenate kinase2.7.1.330.442
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.442
1qjfACSIsopenicillin N synthase1.21.3.10.441
1xzqFONtRNA modification GTPase MnmE3.6.50.441
2i9pNAD3-hydroxyisobutyrate dehydrogenase, mitochondrial1.1.1.310.441
2imkGTXAGAP009194-PA/0.441
2ofv242Tyrosine-protein kinase Lck2.7.10.20.441
2p6iSAHDiphthine synthase/0.441
2vcmM11Isopenicillin N synthase1.21.3.10.441
2vroNDP3,4-dehydroadipyl-CoA semialdehyde dehydrogenase/0.441
2x9dITCTetracycline repressor protein class D/0.441
3dvlATPCircadian clock protein kinase KaiC2.7.11.10.441
3nmpPYVAbscisic acid receptor PYL2/0.441
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4h4o506Gag-Pol polyprotein2.7.7.490.441
4idpGNPAtlastin-13.6.50.441
1hb3SCVIsopenicillin N synthase1.21.3.10.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2huvSAHDiphthine synthase/0.440
2vbdV10Isopenicillin N synthase1.21.3.10.440
2zi63D1Deoxycytidine kinase2.7.1.740.440
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.440
3junAKDPhenazine biosynthesis protein A/B/0.440
3p9tTCLRepressor/0.440
5uviZMAAdenosine receptor A2a/0.440