Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3fbcTYDNucleoside diphosphate kinase2.7.4.6

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3fbcTYDNucleoside diphosphate kinase2.7.4.61.000
3fbeGDPNucleoside diphosphate kinase2.7.4.60.562
3nguADPNucleoside diphosphate kinase/0.525
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.60.503
1buxPPSNucleoside diphosphate kinase, cytosolic2.7.4.60.498
3q8uADPNucleoside diphosphate kinase/0.498
1wklATPNucleoside diphosphate kinase/0.495
3junAKDPhenazine biosynthesis protein A/B/0.494
3v0o4GWHisto-blood group ABO system transferase/0.493
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.490
4yfy1YJVioF/0.484
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.471
3v0p4GWHisto-blood group ABO system transferase/0.471
1nhkCMPNucleoside diphosphate kinase2.7.4.60.469
3uptTPPTransketolase/0.469
5dp2NAPCurF/0.469
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.467
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.467
1tkaN3TTransketolase 12.2.1.10.466
3t8vBTJM1 family aminopeptidase3.4.110.466
4qvhCOAPhosphopantetheinyl transferase PptT (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl-carrier protein]pantetheinephosphotransferase)/0.465
1trkTPPTransketolase 12.2.1.10.464
2r5nTPPTransketolase 1/0.461
3pvcFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.461
5droZH2UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.461
1vyrFMNPentaerythritol tetranitrate reductase/0.460
1xdpATPPolyphosphate kinase/0.459
4nbb9CATerminal oxygenase component of carbazole/0.459
2r8pT6FTransketolase 1/0.458
3cvkN34Genome polyprotein2.7.7.480.458
3epyCOAAcyl-CoA-binding domain-containing protein 7/0.458
3upi0C2Genome polyprotein2.7.7.480.457
3wqmB29Diterpene synthase3.1.7.80.456
1g3mPCQEstrogen sulfotransferase2.8.2.40.455
3hj9FMNUncharacterized protein/0.455
3qiyQI1Botulinum neurotoxin type A3.4.24.690.455
4rquNADAlcohol dehydrogenase class-P/0.454
3c4vLIPD-inositol 3-phosphate glycosyltransferase2.4.1.2500.452
2ycnP61Tyrosine phenol-lyase4.1.99.20.451
2ym2FADPhenylacetone monooxygenase1.14.13.920.451
3b9lAZZSerum albumin/0.451
3ceaNADMyo-inositol 2-dehydrogenase-like (Promiscuous)/0.451
2ptfFMNUncharacterized protein MTH_863/0.450
4dbzNDPPutative ketoacyl reductase1.3.10.450
1z6tADPApoptotic protease-activating factor 1/0.449
3p82FMNPentaerythritol tetranitrate reductase/0.449
4g1nNZTPyruvate kinase PKM2.7.1.400.449
4uy6SAHHistidine N-alpha-methyltransferase/0.449
1h50FMNPentaerythritol tetranitrate reductase/0.448
1z4uPH9Polyprotein/0.448
2hveADPNucleoside diphosphate kinase A2.7.4.60.448
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.448
1cbrREACellular retinoic acid-binding protein 1/0.447
1qxoFMNChorismate synthase/0.447
2ylxFADPhenylacetone monooxygenase1.14.13.920.447
3h59H59Genome polyprotein2.7.7.480.447
3vo8GDPCell division protein FtsZ/0.447
4q5jANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.447
4ugaH4BNitric oxide synthase oxygenase1.14.13.1650.447
1nmkSFMPeptidyl-prolyl cis-trans isomerase A5.2.1.80.446
4a99FADTetX family tetracycline inactivation enzyme/0.446
4iwv1J9Glucokinase2.7.1.20.446
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.445
3h5sH5SGenome polyprotein2.7.7.480.445
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.445
4a6nFADTetX family tetracycline inactivation enzyme/0.445
4bfyZVYPantothenate kinase2.7.1.330.445
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.445
4yfy0FXVioF/0.445
3c6n2S8Protein TRANSPORT INHIBITOR RESPONSE 1/0.444
1ngsTPPTransketolase 12.2.1.10.443
2b9iADPMitogen-activated protein kinase FUS32.7.11.240.443
3p67FMNPentaerythritol tetranitrate reductase/0.443
4la7A1OAbscisic acid receptor PYL2/0.443
1db48INPhospholipase A2, membrane associated/0.442
1stcSTUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2a84ATPPantothenate synthetase6.3.2.10.442
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.442
2jh0701Prothrombin3.4.21.50.442
3gbuATPUncharacterized sugar kinase PH14592.7.10.442
4eaw0NQGenome polyprotein2.7.7.480.442
1cbqRE9Cellular retinoic acid-binding protein 2/0.441
1kquBR4Phospholipase A2, membrane associated/0.441
2b9jADPMitogen-activated protein kinase FUS32.7.11.240.441
2hq9FADMll6688 protein/0.441
2r8oT5XTransketolase 1/0.441
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.441
3u3o3QVSulfotransferase 1A12.8.2.10.441
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.441
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4k5o1OTM1 family aminopeptidase3.4.110.441
5iqiGNPBifunctional AAC/APH2.3.10.441
3dafFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.440
3il4ACO3-oxoacyl-[acyl-carrier-protein] synthase 3/0.440
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.440
3zksWZVBeta-secretase 23.4.23.450.440
4dliIRGMitogen-activated protein kinase 14/0.440
4g2i0VQVitamin D3 receptor/0.440
4h1e10JBeta-secretase 13.4.23.460.440
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.440
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.440
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.440